diff --git a/ot2/octopus-full-ssh.py b/ot2/octopus-full-ssh.py
new file mode 100644
index 0000000..d24d4ed
--- /dev/null
+++ b/ot2/octopus-full-ssh.py
@@ -0,0 +1,664 @@
+from opentrons import protocol_api
+
+
+metadata = {
+    'apiLevel': '2.12',
+    'protocolName': 'OCTOPUS OT-2 Protocol: SSH-compatible, All Stages, Offset Calibrated',
+    'author': 'Octant',
+    'description': 'v1.0.0'
+}
+
+
+def run(protocol: protocol_api.ProtocolContext):
+    """
+    OT-2 Protocol for running select steps of the Twist 96-Plex protocol 
+    (formally iGenomX RIPTIDE) adapted for OCTOPUS and sequencing on 
+    Illumina MiSeq with the MiSeq Reagent Micro Kit v2 (300-cycles).
+
+    After running the main thermocycler protocol in "A Reaction" and adding EDTA, 
+    the samples can thereafter be processed by the OT-2 for the rest of 
+    the Twist 96-Plex protocol up to final validation/quantification 
+    for sequencer loading.
+
+    This specific layout allows for running on the OT-2 directly through SSH, 
+    includes offset-calibration templates, and runs through all stages.
+
+    The following equipment/labware are assumed:
+    1x  8-Channel P300 (GEN2)
+    1x  8-Channel P20 (GEN2)
+    1x  Magnetic Module
+    4x  Opentrons 96 Filter Tip Rack 200 uL
+    1x  Opentrons 96 Filter Tip Rack 20 uL
+    3x  Bio-Rad 96 Well Plate 200 uL PCR
+    2x  Applied Biosystems MicroAmp 384 Well Plate 40 uL
+    1x  NEST 96 Deepwell Plate 2mL
+    """
+    ### specify the number of plates to process: integer between 1 and 8 inclusive
+    number_of_plates = 0
+    ### specify True if running protocol on OT-2 command line, otherwise False
+    ssh_mode = True
+
+    protocol.set_rail_lights(True)
+    Run = OCTOPUS(protocol, ssh_mode)
+    Run.Pool(number_of_plates)
+    Run.Post_Pool()
+    protocol.set_rail_lights(False)
+
+
+class OCTOPUS:
+    """The OCTOPUS class serves as a container for all steps of Twist 96-Plex protocol that can involve the OT-2.
+
+    It splits the overall protocol into two stages: Pool and Post-pool. From the perspective of the OT-2, these
+    stages differ in which labware the Magnetic Module holds. The Pool Stage steps require larger reagent volumes, 
+    requiring a large plate. Once space on that plate is exhausted, a smaller plate that is more size appropriate 
+    replaces it for the duration of the Post-pool Stage.
+
+    The state of SSH Mode is required since this mode is incompatible with the Opentrons App as of Server Version 5.0.2.
+
+    Each OT-2 robot will have its own offset-calibration numbers. The ones here are only for the OT-2 used at Octant. 
+    To determine the offset calibrations one's own OT-2, Opentrons has the following guide:
+    https://support.opentrons.com/en/articles/5901728-how-to-prepare-jupyter-notebook-and-opentrons_execute-for-5-0-0
+    """
+    def __init__(self, protocol, ssh_mode=False):
+        ### tip-rack definitions
+            # opentrons 200 ul filtered tips
+        tips_200_1 = protocol.load_labware('opentrons_96_filtertiprack_200ul', '7')
+        tips_200_2 = protocol.load_labware('opentrons_96_filtertiprack_200ul', '8')
+        tips_200_3 = protocol.load_labware('opentrons_96_filtertiprack_200ul', '10')
+        tips_200_4 = protocol.load_labware('opentrons_96_filtertiprack_200ul', '11')
+            # opentrons 20 ul filtered tips
+        tips_20_1 = protocol.load_labware('opentrons_96_filtertiprack_20ul', '3') 
+
+        if ssh_mode:
+            tips_200_1.set_offset(x=-0.60, y=1.00, z=-0.20)
+            tips_200_2.set_offset(x=-0.60, y=1.00, z=-0.20)
+            tips_200_3.set_offset(x=-0.60, y=1.00, z=-0.20)
+            tips_200_4.set_offset(x=-0.60, y=1.00, z=-0.20)
+            tips_20_1.set_offset(x=0.00, y=1.00, z=-0.10)
+
+        self.tips_200 = [tips_200_1, tips_200_2, tips_200_3, tips_200_4]
+        self.tips_20 = [tips_20_1]
+
+        ### pipette definitions
+        self.p300 = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=self.tips_200)
+        self.p20 = protocol.load_instrument('p20_multi_gen2', 'right', tip_racks=self.tips_20)
+
+        ### load magnetic module
+        self.mag_mod = protocol.load_module('magnetic module gen2', '9')
+
+        ### pass down protocol api throughout object
+        self.protocol = protocol
+
+        ### pass down ssh-mode status throughout object
+        self.ssh_mode = ssh_mode
+
+    def Pool(self, num_plates=0):
+        """Pool Stage.
+
+        The OT-2 takes over after EDTA has been added to the 384-well Reaction A Plates containing the plate samples.
+
+        The Magnetic Module holds a deep-well plate during this stage.
+
+        Arguments:
+        num_plates -- Specifies how many plates to pool. This defaults to an exception.
+        """
+        NUM_PLATES = num_plates
+        if NUM_PLATES < 1 or NUM_PLATES > 8:
+            raise Exception("Error: Number of plates must be between 1 and 8 inclusive.")
+
+        ### labware specific to Pool stage
+        self.pool_plate = self.mag_mod.load_labware('nest_96_wellplate_2ml_deep', label='Pool Plate')
+        self.dna_plate = self.protocol.load_labware('biorad_96_wellplate_200ul_pcr', '6', label='DNA Plate')
+        self.consolidation_plate = self.protocol.load_labware('biorad_96_wellplate_200ul_pcr', '4', label='Consolidation Plate')
+        self.pre_pool_plate_1 = self.protocol.load_labware('appliedbiosystems_384_wellplate_40ul', '1', label='Pre-pool Plate 1 (1-4)')
+        self.pre_pool_plate_2 = self.protocol.load_labware('appliedbiosystems_384_wellplate_40ul', '2', label='Pre-pool Plate 2 (5-8)')
+
+        SSH_MODE = self.ssh_mode
+        if SSH_MODE:
+            self.pool_plate.set_offset(x=0.10, y=1.60, z=0.00)
+            self.dna_plate.set_offset(x=0.40, y=1.10, z=0.10)
+            self.consolidation_plate.set_offset(x=0.10, y=1.10, z=0.00)
+            self.pre_pool_plate_1.set_offset(x=0.00, y=0.80, z=0.60)
+            self.pre_pool_plate_2.set_offset(x=0.00, y=0.80, z=0.60)
+
+        ### reagent locations
+        DNA_pool = self.pool_plate.wells_by_name()['A1']
+        Purification_Beads = self.pool_plate.wells_by_name()['A3']
+        Purification_Beads_discard = self.pool_plate.wells_by_name()['A4']
+        Ethanol = [self.pool_plate.wells_by_name()['A6'], self.pool_plate.wells_by_name()['A9']]
+        Ethanol_discard = [self.pool_plate.wells_by_name()['A7'], self.pool_plate.wells_by_name()['A10']]
+        Tris_HCl = self.pool_plate.wells_by_name()['A12']
+
+        ### consolidate Reaction A plate after iGenomX_1 into consolidation plate
+        self.set_flow_rate(48, 48, 48)
+            # consolidating VE plates 1-4 to Pool Plate columns 1-4
+        if NUM_PLATES >= 1:
+            self.p300.consolidate(5, [self.pre_pool_plate_1.rows_by_name()['A'][num_plate].bottom(z=0.5) for num_plate in range(0, 23, 2)], self.consolidation_plate.columns('1'))
+        if NUM_PLATES >= 2:
+            self.p300.consolidate(5, [self.pre_pool_plate_1.rows_by_name()['A'][num_plate].bottom(z=0.5) for num_plate in range(1, 24, 2)], self.consolidation_plate.columns('2'))
+        if NUM_PLATES >= 3:
+            self.p300.consolidate(5, [self.pre_pool_plate_1.rows_by_name()['B'][num_plate].bottom(z=0.5) for num_plate in range(0, 23, 2)], self.consolidation_plate.columns('3'))
+        if NUM_PLATES >= 4:
+            self.p300.consolidate(5, [self.pre_pool_plate_1.rows_by_name()['B'][num_plate].bottom(z=0.5) for num_plate in range(1, 24, 2)], self.consolidation_plate.columns('4'))
+            # consolidating VE plates 5-8 to Pool Plate columns 5-8
+        if NUM_PLATES >= 5:
+            self.p300.consolidate(5, [self.pre_pool_plate_2.rows_by_name()['A'][num_plate].bottom(z=0.5) for num_plate in range(0, 23, 2)], self.consolidation_plate.columns('5'))
+        if NUM_PLATES >= 6:
+            self.p300.consolidate(5, [self.pre_pool_plate_2.rows_by_name()['A'][num_plate].bottom(z=0.5) for num_plate in range(1, 24, 2)], self.consolidation_plate.columns('6'))
+        if NUM_PLATES >= 7:
+            self.p300.consolidate(5, [self.pre_pool_plate_2.rows_by_name()['B'][num_plate].bottom(z=0.5) for num_plate in range(0, 23, 2)], self.consolidation_plate.columns('7'))
+        if NUM_PLATES == 8:
+            self.p300.consolidate(5, [self.pre_pool_plate_2.rows_by_name()['B'][num_plate].bottom(z=0.5) for num_plate in range(1, 24, 2)], self.consolidation_plate.columns('8'))
+
+        ### further consolidate plate columns into single wells on the DNA pool deep well plate
+        self.set_flow_rate(48*2, 48, 48)
+        for i in range(NUM_PLATES):
+            self.p300.pick_up_tip(self.tips_200[0].rows()[7-i][NUM_PLATES])
+            # aspirate first four wells
+            for j in range(4):
+                self.p300.aspirate(50, self.consolidation_plate.rows()[j][i].bottom(z=0.5))
+            self.p300.dispense(200, self.pool_plate.rows()[i][0])
+            # aspirate last four wells
+            for j in range(4):
+                self.p300.aspirate(50, self.consolidation_plate.rows()[j+4][i].bottom(z=0.5))
+            self.p300.dispense(200, self.pool_plate.rows()[i][0])
+            self.p300.drop_tip()
+
+        ### add and incubate Purification Beads with pooled samples
+        self.p300.pick_up_tip()
+        self.set_flow_rate(48*4, 48*4, 48)
+        self.p300.mix(10, 200, Purification_Beads.bottom(z=10.0))
+            # adding beads to pool
+        self.set_flow_rate(48*2, 48*4, 48)
+        for i in range(3):
+            self.p300.aspirate(200, Purification_Beads)
+            self.p300.dispense(200, DNA_pool)
+        self.p300.aspirate(120, Purification_Beads)
+        self.p300.dispense(120, DNA_pool)
+            # mix beads well with pool and incubate
+        self.set_flow_rate(48*4, 48*6, 48)
+        self.p300.mix(10, 200, DNA_pool.bottom(z=10.0))
+        self.set_flow_rate(48*4, 48*4, 48)
+        for i in range(20):
+            self.p300.aspirate(200, DNA_pool.bottom(z=10.0))
+            self.p300.dispense(200, DNA_pool.center())
+        self.set_flow_rate(48*4, 48*6, 48/6)
+        self.p300.mix(20, 200, DNA_pool.bottom(z=10.0))
+        self.p300.move_to(DNA_pool.top())
+        self.protocol.delay(seconds=5.0)
+        self.p300.blow_out(DNA_pool.top())
+        self.p300.drop_tip()
+        self.protocol.delay(minutes=10)
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=12)
+
+        ### discard supernatant in stages to minimize bead loss
+        self.set_flow_rate(48/2, 48, 48)
+        self.p300.pick_up_tip()
+        self.p300.aspirate(200, DNA_pool.bottom(z=0.5))
+        self.p300.dispense(200, Purification_Beads_discard)
+        self.p300.move_to(Purification_Beads_discard.top(z=10.0))
+        self.protocol.delay(minutes=4)
+        self.p300.aspirate(200, DNA_pool.bottom(z=0.5))
+        self.p300.dispense(200, Purification_Beads_discard)
+        self.p300.move_to(Purification_Beads_discard.top(z=10.0))
+        self.protocol.delay(minutes=2)
+        self.p300.aspirate(200, DNA_pool.bottom(z=0.5))
+        self.p300.dispense(200, Purification_Beads_discard)
+        self.p300.move_to(Purification_Beads_discard.top(z=10.0))
+        self.protocol.delay(minutes=2)
+        self.p300.aspirate(200, DNA_pool.bottom(z=0.5))
+        self.p300.dispense(200, Purification_Beads_discard)
+        self.p300.move_to(Purification_Beads_discard.top(z=10.0))
+        self.protocol.delay(minutes=2)
+        self.p300.aspirate(200, DNA_pool.bottom(z=0.5))
+        self.p300.dispense(200, Purification_Beads_discard)
+        self.p300.move_to(Purification_Beads_discard.top(z=10.0))
+        self.protocol.delay(minutes=2)
+        self.p300.aspirate(120, DNA_pool.bottom(z=0.5))
+        self.p300.dispense(120, Purification_Beads_discard)
+        self.p300.drop_tip()
+        self.set_flow_rate(5, 48, 48)
+        self.p20.pick_up_tip()
+        self.p20.aspirate(20, DNA_pool.bottom())
+        self.p20.drop_tip()
+
+        ### wash with 80% ethanol twice
+        self.set_flow_rate(48, 48, 48)
+        self.p300.pick_up_tip()
+        for i in range(6):
+            self.p300.aspirate(200, Ethanol[0])
+            self.p300.dispense(200, DNA_pool.top(z=-10.0))
+        self.p300.move_to(DNA_pool.top(z=10.0))
+        self.protocol.delay(seconds=40)
+        self.discard_supernatant(1200, DNA_pool, Ethanol_discard[0].top(z=-10.0))
+            # second time
+        self.set_flow_rate(48, 48, 48)
+        self.p300.pick_up_tip()
+        for i in range(6):
+            self.p300.aspirate(200, Ethanol[1])
+            self.p300.dispense(200, DNA_pool.top(z=-10.0))
+        self.p300.move_to(DNA_pool.top(z=10.0))
+        self.protocol.delay(seconds=40)
+        self.discard_supernatant(1200, DNA_pool, Ethanol_discard[1].top(z=-10.0))
+
+        ### discard residual ethanol and let dry in stages to maximize ethanol removal
+        self.set_flow_rate(5, 48, 48)
+        self.p20.pick_up_tip()
+        self.p20.aspirate(20, DNA_pool.bottom(z=-0.5))
+        self.p20.drop_tip()
+        self.protocol.delay(minutes=10)
+        self.set_flow_rate(1, 48, 48)
+        self.p20.pick_up_tip()
+        self.p20.aspirate(5, DNA_pool.bottom(z=-0.5))
+        self.p20.drop_tip()
+        self.protocol.delay(minutes=5)
+        self.set_flow_rate(1, 48, 48)
+        self.p20.pick_up_tip()
+        self.p20.aspirate(5, DNA_pool.bottom(z=-1.0))
+        self.p20.drop_tip()
+
+        ### resuspend beads well in 10 mM Tris-HCl pH 8
+        self.mag_mod.disengage()
+        self.set_flow_rate(48, 48, 48)
+        self.p300.pick_up_tip()
+        self.p300.aspirate(50, Tris_HCl.bottom(z=0.5))
+        self.p300.dispense(50, DNA_pool)
+        self.set_flow_rate(48, 48*2, 48/2)
+        self.p300.mix(20, 30, DNA_pool.bottom(z=1.0))
+        self.set_flow_rate(48/4, 48/4, 48/2)
+        self.p300.mix(5, 45, DNA_pool.bottom(z=1.0))
+        self.set_flow_rate(48, 48, 48)
+        for i in range(20):
+            self.p300.aspirate(30, DNA_pool.bottom(z=1.0))
+            self.p300.dispense(30, DNA_pool.bottom(z=5.0))
+        self.set_flow_rate(48/4, 48/4, 48/2)
+        self.p300.mix(5, 45, DNA_pool.bottom(z=1.0))
+        self.set_flow_rate(48, 48*2, 48/2)
+        self.p300.mix(30, 30, DNA_pool.bottom(z=1.0))
+        self.p300.blow_out(DNA_pool.bottom(z=5.0))
+        self.p300.move_to(DNA_pool.top(z=10.0))
+        self.protocol.delay(minutes=5)
+            # resuspend settled beads
+        self.set_flow_rate(48/4, 48/4, 48/2)
+        self.p300.mix(5, 45, DNA_pool.bottom(z=1.0))
+        self.set_flow_rate(48, 48, 48)
+        for i in range(10):
+            self.p300.aspirate(30, DNA_pool.bottom(z=1.0))
+            self.p300.dispense(30, DNA_pool.bottom(z=5.0))
+        self.set_flow_rate(48/4, 48/4, 48/2)
+        self.p300.mix(5, 45, DNA_pool.bottom(z=1.0))
+        self.set_flow_rate(48, 48*2, 48/2)
+        self.p300.mix(30, 30, DNA_pool.bottom(z=1.0))
+        self.p300.blow_out(DNA_pool.bottom(z=5.0))
+        self.p300.drop_tip()
+        self.protocol.delay(minutes=5)
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=4)
+
+        ### end of Pool Stage, prepare for Post-pool Stage
+        self.set_flow_rate(48/4, 48, 48)
+        self.p300.transfer(50, DNA_pool, self.dna_plate.wells_by_name()['A1'], blow_out=True, blowout_location='destination well')
+        self.set_flow_rate(1, 5, 5)
+        self.p20.pick_up_tip()
+        self.p20.aspirate(10, DNA_pool.bottom())
+        self.p20.dispense(5, self.dna_plate.wells_by_name()['A1'].top(z=-5.0))
+        self.p20.dispense(5, self.dna_plate.wells_by_name()['A1'])
+        self.p20.blow_out(self.dna_plate.wells_by_name()['A1'].top())
+        self.p20.drop_tip()
+        if SSH_MODE:
+            input('Execute thermocycler protocol "iGenomX_Pre" on the DNA Plate. Replace former DNA Plate slot with plate containing Post-pool reagents. Empty trash contents if necessary. Discard deep-well plate. Afterward, spin down and secure DNA Plate on the Magnetic Module. Resume protocol for Post-pool stage. (Press ENTER)')
+            input("ARE YOU SURE? Press ENTER to continue.")
+        else:
+            self.protocol.pause('Execute thermocycler protocol "iGenomX_Pre" on the DNA Plate. Replace former DNA Plate slot with plate containing Post-pool reagents. Empty trash contents if necessary. Discard deep-well plate. Afterward, spin down and secure DNA Plate on the Magnetic Module. Resume protocol for Post-pool stage.')
+        self.mag_mod.disengage()
+        self.protocol.home()
+
+    def Post_Pool(self):
+        """Post-pool Stage.
+
+        Corresponds to the following steps from Twist 96-Plex protocol:
+        Step 2: DNA Capture and Library Conversion
+        Step 3: Amplification
+        Step 4: Purification and Size Selection
+
+        The Magnetic Module holds a PCR plate during this stage.
+
+        Note that this stage operates independently from the number of plates for the run since the plates 
+        are assumed to have already consolidated to a single column.
+        """
+        ### redefine labware placements specific to Post-pool stage
+        self.protocol.deck['9']._labware = None
+        self.dna_plate = self.mag_mod.load_labware('biorad_96_wellplate_200ul_pcr', label='DNA Plate')
+        del self.protocol.deck['6']
+        self.post_pool_reagents = self.protocol.load_labware('biorad_96_wellplate_200ul_pcr', '6', label='Post-pool Reagents Plate')
+
+        SSH_MODE = self.ssh_mode
+        if SSH_MODE:
+            self.dna_plate.set_offset(x=0.40, y=1.20, z=0.20)
+            self.post_pool_reagents.set_offset(x=0.60, y=0.90, z=0.10)
+
+        ### partition Post-pool stage into substages
+        self.DNA_Capture_Library_Conversion()
+        self.Library_Amplification()
+        self.Size_Selection()
+
+    def DNA_Capture_Library_Conversion(self):
+        """Perform capture of extended terminated ssDNA library followed by conversion to dsDNA."""
+        SSH_MODE = self.ssh_mode
+
+        ### reagent locations
+        Capture_Beads = self.post_pool_reagents.wells_by_name()['A1']
+        HS_Buffer = self.post_pool_reagents.wells_by_name()['A2']
+        NaOH = self.post_pool_reagents.wells_by_name()['A3']
+        Bead_Wash_Buffer = [self.post_pool_reagents.wells_by_name()['A4'], self.post_pool_reagents.wells_by_name()['A4'], self.post_pool_reagents.wells_by_name()['A5']]
+
+        ### prepare Capture Beads
+        if SSH_MODE:
+            input('Manually add 20 ul Capture Beads to column 2 of DNA Plate for each plate.')
+            input("ARE YOU SURE? Press ENTER to continue.")
+        else:
+            self.protocol.pause('Manually add 20 ul Capture Beads down column 2 of DNA Plate for each plate.')
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=4)
+        #self.discard_supernatant(20, self.dna_plate.wells_by_name()['A2'])
+        self.set_flow_rate(48/6, 48, 48)
+        self.p300.pick_up_tip()
+        self.p300.aspirate(20, self.dna_plate.wells_by_name()['A2'].bottom(z=0.5))
+        self.p300.drop_tip()
+        self.mag_mod.disengage()
+            # wash with HS buffer
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.transfer(100, HS_Buffer, self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_after=(10,100))
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=10)
+        self.discard_supernatant(100, self.dna_plate.wells_by_name()['A2'])
+        self.mag_mod.disengage()
+            # resuspend in HS buffer
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.transfer(20, HS_Buffer, self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_after=(10,15))
+
+        ### add pool samples into the Capture Beads
+        self.set_flow_rate(48/4, 48, 48)
+        self.p300.pick_up_tip()
+        self.p300.aspirate(50, self.dna_plate.wells_by_name()['A1'].bottom(z=0.5))
+        self.p300.dispense(50, self.dna_plate.wells_by_name()['A2'])
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.mix(10, 65, self.dna_plate.wells_by_name()['A2'])
+        self.p300.blow_out(self.dna_plate.wells_by_name()['A2'].top())
+        self.p300.move_to(self.dna_plate.wells_by_name()['A2'].top(z=10.0))
+        self.protocol.delay(minutes=10)
+            # resuspend same well again
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.mix(10, 65, self.dna_plate.wells_by_name()['A2'])
+        self.p300.blow_out(self.dna_plate.wells_by_name()['A2'].top())
+        self.p300.drop_tip()
+        self.protocol.delay(minutes=10)
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=10)
+        self.discard_supernatant(70, self.dna_plate.wells_by_name()['A2'])
+        self.mag_mod.disengage()
+
+        ### denature with NaOH
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.transfer(100, NaOH, self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_before=(3,95), mix_after=(10,95))
+        self.protocol.delay(minutes=4)
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=5)
+        self.discard_supernatant(100, self.dna_plate.wells_by_name()['A2'])
+        self.mag_mod.disengage()
+        self.set_flow_rate(48*2, 48*4, 48)
+
+        ### wash with Bead Wash Buffer three times
+        self.p300.transfer(100, Bead_Wash_Buffer[0], self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_after=(10,95))
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=4)
+        self.discard_supernatant(100, self.dna_plate.wells_by_name()['A2'])
+        self.mag_mod.disengage()
+            # second time
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.transfer(100, Bead_Wash_Buffer[1], self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_after=(10,95))
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=4)
+        self.discard_supernatant(100, self.dna_plate.wells_by_name()['A2'])
+        self.mag_mod.disengage()
+            # third time
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.transfer(100, Bead_Wash_Buffer[2], self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_after=(10,95))
+        self.mag_mod.engage(height=11.0)
+        self.protocol.delay(minutes=4)
+        if SSH_MODE:
+            input('Resume to complete wash step.')
+            input("ARE YOU SURE? Press ENTER to continue.")
+        else:
+            self.protocol.pause('Resume to complete wash step.')
+        self.discard_supernatant(100, self.dna_plate.wells_by_name()['A2'])
+        self.discard_residual(self.dna_plate.wells_by_name()['A2'])
+
+        ### proceed with Reaction B 
+        if SSH_MODE:
+            input('Resuspend each well in 18.5 ul Reaction B mix (without enzyme). Then, mix 0.5 ul Enzyme II into each well. Execute thermocycler protocol "iGenomX_2". Afterward, secure DNA Plate back on the Magnetic Module. Resume protocol. (Press ENTER)')
+            input("ARE YOU SURE? Press ENTER to continue.")
+        else:
+            self.protocol.pause('Resuspend each well in 18.5 ul Reaction B mix (without enzyme). Then, mix 0.5 ul Enzyme II into each well. Execute thermocycler protocol "iGenomX_2". Afterward, secure DNA Plate back on the Magnetic Module. Resume protocol.')
+        self.mag_mod.disengage()
+        self.protocol.home()
+
+    def Library_Amplification(self):
+        """Amplify libraries using universal and index specific amplification primers."""
+        SSH_MODE = self.ssh_mode
+
+        ### reagent locations
+        Bead_Wash_Buffer = [self.post_pool_reagents.wells_by_name()['A6'], self.post_pool_reagents.wells_by_name()['A6'], self.post_pool_reagents.wells_by_name()['A7']]
+
+        ### resuspend beads after coming off thermocycler and discard reaction
+        self.set_flow_rate(48*2, 48*6, 48)
+        self.p300.pick_up_tip()
+        self.p300.mix(10, 15, self.dna_plate.wells_by_name()['A2'])
+        self.p300.blow_out(self.dna_plate.wells_by_name()['A2'].top())
+        self.p300.drop_tip()
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=4)
+        self.discard_supernatant(19, self.dna_plate.wells_by_name()['A2'])
+        self.mag_mod.disengage()
+
+        ### wash with Bead Wash Buffer three times
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.transfer(100, Bead_Wash_Buffer[0], self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_after=(10,95))
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=4)
+        self.discard_supernatant(100, self.dna_plate.wells_by_name()['A2'])
+        self.mag_mod.disengage()
+            # second time
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.transfer(100, Bead_Wash_Buffer[1], self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_after=(10,95))
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=4)
+        self.discard_supernatant(100, self.dna_plate.wells_by_name()['A2'])
+        self.mag_mod.disengage()
+            # third time
+        self.set_flow_rate(48*2, 48*4, 48)
+        self.p300.transfer(100, Bead_Wash_Buffer[2], self.dna_plate.wells_by_name()['A2'], blow_out=True, blowout_location='destination well', mix_after=(10,95))
+        self.mag_mod.engage(height=11.0)
+        self.protocol.delay(minutes=4)
+        if SSH_MODE:
+            input('Resume to complete wash step.')
+            input("ARE YOU SURE? Press ENTER to continue.")
+        else:
+            self.protocol.pause('Resume to complete wash step.')
+        self.discard_supernatant(100, self.dna_plate.wells_by_name()['A2'])
+        self.discard_residual(self.dna_plate.wells_by_name()['A2'])
+
+        ### proceed with Amplification "Reaction C"
+        if SSH_MODE:
+            input('Resuspend each well in 50 ul Amplification "Reaction C" mix (primers added). Be sure to record which wells received which index primer. Execute thermocycler protocol "iGenomx_PCR". Afterward, secure DNA Plate back on the Magnetic Module. Resume protocol. (Press ENTER)')
+            input("ARE YOU SURE? Press ENTER to continue.")
+        else:
+            self.protocol.pause('Resuspend each well in 50 ul Amplification "Reaction C" mix (primers added). Be sure to record which wells received which index primer. Execute thermocycler protocol "iGenomx_PCR". Afterward, secure DNA Plate back on the Magnetic Module. Resume protocol.')
+        self.mag_mod.disengage()
+        self.protocol.home()
+
+        ### prepare for bead-based size selection
+        self.set_flow_rate(48/4, 48, 48)
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=8)
+        self.p300.transfer(50, self.dna_plate.wells_by_name()['A2'].bottom(z=0.5), self.dna_plate.wells_by_name()['A3'])
+        self.mag_mod.disengage()
+
+    def Size_Selection(self):
+        """Purification of DNA libraries and double sided size selection.
+
+        Volumes optimized for 2 x 150 read lengths for Illumina MiSeq.
+        """
+        SSH_MODE = self.ssh_mode
+
+        ### reagent locations
+        Purification_Beads = self.post_pool_reagents.wells_by_name()['A8']
+        Ethanol = [self.post_pool_reagents.wells_by_name()['A9'], self.post_pool_reagents.wells_by_name()['A10']]
+        IDTE = self.post_pool_reagents.wells_by_name()['A12']
+
+        ### first round of size selection (removes large reads)
+        self.p300.pick_up_tip()
+        self.set_flow_rate(48*3, 48*3, 48)
+        self.p300.mix(10, 35, Purification_Beads)
+        self.set_flow_rate(48, 48, 48)
+        self.p300.aspirate(32.5, Purification_Beads)
+        self.p300.dispense(32.5, self.dna_plate.wells_by_name()['A3'])
+        self.set_flow_rate(48*3, 48*3, 48)
+        self.p300.mix(10, 50, self.dna_plate.wells_by_name()['A3'])
+        self.set_flow_rate(48, 48, 48)
+        for i in range(5):
+            self.p300.aspirate(50, self.dna_plate.wells_by_name()['A3'].bottom(z=1.0))
+            self.p300.dispense(50, self.dna_plate.wells_by_name()['A3'].center())
+        self.set_flow_rate(48*3, 48*3, 48)
+        self.p300.mix(10, 50, self.dna_plate.wells_by_name()['A3'])
+        self.p300.blow_out(self.dna_plate.wells_by_name()['A3'].top())
+        self.p300.drop_tip()
+        self.protocol.delay(minutes=10)
+        self.mag_mod.engage(height=11.0)
+        self.protocol.delay(minutes=6)
+        self.set_flow_rate(48/4, 48/2, 48/2)
+        self.p300.transfer(65, self.dna_plate.wells_by_name()['A3'], self.dna_plate.wells_by_name()['A4'], blow_out=True, blowout_location='destination well')
+        self.set_flow_rate(1, 5, 5)
+        self.p20.pick_up_tip()
+        self.p20.aspirate(15, self.dna_plate.wells_by_name()['A3'].bottom())
+        self.p20.dispense(10, self.dna_plate.wells_by_name()['A4'].top(z=-5.0))
+        self.p20.dispense(5, self.dna_plate.wells_by_name()['A4'])
+        self.p20.blow_out(self.dna_plate.wells_by_name()['A4'].top())
+        self.p20.drop_tip()
+        self.mag_mod.disengage()
+
+        ### second round of size selection (removes small reads)
+        self.p20.pick_up_tip()
+        self.set_flow_rate(10, 40, 10)
+        self.p20.mix(10, 10, Purification_Beads)
+        self.set_flow_rate(10/2, 10/2, 10)
+        self.p20.aspirate(10, Purification_Beads)
+        self.p20.dispense(10, self.dna_plate.wells_by_name()['A4'])
+        self.set_flow_rate(10*2, 10*2, 10)
+        self.p20.mix(10, 20, self.dna_plate.wells_by_name()['A4'])
+        self.set_flow_rate(10*2, 10*2, 10)
+        for i in range(20):
+            self.p20.aspirate(20, self.dna_plate.wells_by_name()['A4'].bottom(z=1.0))
+            self.p20.dispense(20, self.dna_plate.wells_by_name()['A4'].top(z=-5.0))
+        self.set_flow_rate(10*2, 10*2, 10)
+        self.p20.mix(10, 20, self.dna_plate.wells_by_name()['A4'])
+        self.p20.blow_out(self.dna_plate.wells_by_name()['A4'].top())
+        self.p20.drop_tip()
+        self.protocol.delay(minutes=10)
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=6)
+            # discard supernatant in empty column in case significant amount of beads are aspirated away
+        self.set_flow_rate(48/4, 48/4, 48/4)
+        self.p300.transfer(70, self.dna_plate.wells_by_name()['A4'], self.dna_plate.wells_by_name()['A7'], blow_out=True, blowout_location='destination well')
+
+        ### wash with 80% ethanol twice
+        self.set_flow_rate(48, 48, 48)
+        self.p300.pick_up_tip()
+        self.p300.aspirate(150, Ethanol[0])
+        self.p300.dispense(150, self.dna_plate.wells_by_name()['A4'])
+        self.p300.move_to(self.dna_plate.wells_by_name()['A4'].top(z=10.0))
+        self.protocol.delay(seconds=40)
+        self.discard_supernatant(150, self.dna_plate.wells_by_name()['A4'])
+            # second time
+        self.set_flow_rate(48, 48, 48)
+        self.p300.pick_up_tip()
+        self.p300.aspirate(150, Ethanol[1])
+        self.p300.dispense(150, self.dna_plate.wells_by_name()['A4'])
+        self.p300.move_to(self.dna_plate.wells_by_name()['A4'].top(z=10.0))
+        self.protocol.delay(seconds=40)
+        self.discard_supernatant(150, self.dna_plate.wells_by_name()['A4'])
+            # guarantee discard of residual ethanol
+        self.set_flow_rate(1, 48, 48)
+        self.p20.pick_up_tip()
+        self.p20.aspirate(15, self.dna_plate.wells_by_name()['A4'].bottom(z=-0.5))
+        self.p20.drop_tip()
+        self.set_flow_rate(48, 48, 48)
+        self.protocol.delay(seconds=30)
+        self.mag_mod.disengage()
+
+        ### elute in IDTE
+        self.set_flow_rate(48, 48, 48)
+        self.p300.pick_up_tip()
+        self.p300.aspirate(15, IDTE)
+        self.p300.dispense(15, self.dna_plate.wells_by_name()['A4'])
+        self.set_flow_rate(48*2, 48*6, 48)
+        self.p300.mix(10, 20, self.dna_plate.wells_by_name()['A4'])
+        self.p300.blow_out(self.dna_plate.wells_by_name()['A4'].top())
+        self.p300.move_to(self.dna_plate.wells_by_name()['A4'].top(z=10.0))
+        self.protocol.delay(minutes=5)
+            # resuspend settled beads
+        self.p300.mix(10, 20, self.dna_plate.wells_by_name()['A4'])
+        self.p300.blow_out(self.dna_plate.wells_by_name()['A4'].top())
+        self.p300.drop_tip()
+        self.protocol.delay(minutes=5)
+        if SSH_MODE:
+            input('Resume to magstand final elution.')
+            input("ARE YOU SURE? Press ENTER to continue.")
+        else:
+            self.protocol.pause('Resume to magstand final elution.')
+        self.mag_mod.engage()
+        self.protocol.delay(minutes=5)
+
+        ### prepare for NGS prep
+        self.set_flow_rate(12, 16, 16)
+        self.p20.transfer(12, self.dna_plate.wells_by_name()['A4'].bottom(z=0.5), self.dna_plate.wells_by_name()['A12'])
+        self.mag_mod.disengage()
+        self.protocol.home()
+
+    def set_flow_rate(self, aspirate=96, dispense=96, blow_out=96):
+        """Set the speeds (in uL/s) for all pipettes."""
+        self.p300.flow_rate.aspirate = aspirate
+        self.p300.flow_rate.dispense = dispense
+        self.p300.flow_rate.blow_out = blow_out
+        self.p20.flow_rate.aspirate = aspirate
+        self.p20.flow_rate.dispense = dispense
+        self.p20.flow_rate.blow_out = blow_out
+
+    def discard_supernatant(self, vol, well, trash=None):
+        """Discard liquid from wells using the P300 multi-channel."""
+        if trash is None:
+            trash = self.protocol.fixed_trash['A1']
+        if not self.p300.has_tip:
+            self.p300.pick_up_tip()
+        self.set_flow_rate(48/2, 48, 48)
+        while vol > 0:
+            if vol < 200:
+                self.p300.aspirate(vol, well.bottom(z=0.5))
+                self.p300.dispense(vol, trash)
+            else:
+                self.p300.aspirate(200, well.bottom(z=0.5))
+                self.p300.dispense(200, trash)
+            vol = vol - 200
+        self.p300.drop_tip()
+        self.set_flow_rate(48, 48, 48)
+
+    def discard_residual(self, well):
+        """Discard remaining liquid from wells using the P20 multi-channel."""
+        self.set_flow_rate(1, 48, 48)
+        self.p20.pick_up_tip()
+        self.p20.aspirate(5, well.bottom())
+        self.set_flow_rate(1/2, 48, 48)
+        self.p20.aspirate(2, well.bottom(z=-0.5))
+        self.p20.drop_tip()
+        self.set_flow_rate(48, 48, 48)