software list

# samtools 1.9
/opt/conda/envs/rgi/bin/samtools

# bwa 0.7.18-r1243-dirty
/opt/conda/envs/rgi/bin/bwa

# bowtie2  2.5.4
export PATH=/opt/conda/envs/rgi/bin/:$PATH && bowtie2

# bedtools v2.31.1
/opt/conda/envs/rgi/bin/bedtools

# bamtools 2.5.1
/opt/conda/envs/rgi/bin/bamtools

# diamond 2.1.10
 /opt/conda/bin/diamond

# PEAR v0.9.6- Paired-End reAd mergeR
/opt/conda/bin/pear

# blast+ 2.16.0+
/opt/conda/envs/rgi/bin/blastn
/opt/conda/envs/rgi/bin/blastp
/opt/conda/envs/rgi/bin/blastx
/opt/conda/envs/rgi/bin/makeblastdb

# kma KMA-1.4.15
/opt/conda/envs/rgi/bin/kma

# prodigal v2.6.3
/opt/conda/envs/rgi/bin/prodigal

# rgi 6.0.3
/opt/conda/envs/rgi/bin/rgi

# fastANI version 1.32
/opt/conda/envs/gtdbtk/bin/fastANI

#HMMER 3.4
/opt/conda/envs/gtdbtk/bin/hmmscan

# bcftools 1.20 
/opt/conda/bin/bcftools

# CD-HIT version 4.8.1
/opt/conda/bin/cd-hit

#Kraken version 2.1.3
export PATH=/opt/conda/bin/:$PATH && kraken2

#krakentools
export PATH=/opt/conda/bin/:$PATH && kreport2krona.py

# seqtk 1.4-r122
/opt/conda/bin/seqtk

# FastQC
/opt/conda/bin/fastqc

# fastp version 0.23.4
/opt/conda/bin/fastp

# trimmomatic 0.39
/opt/conda/bin/trimmomatic

# cutadapt version 4.9
/opt/conda/bin/cutadapt

# Bracken v2.9
/opt/conda/bin/bracken

# QUAST: Quality Assessment Tool for Genome Assemblies Version: 5.2.0
/opt/conda/bin/quast.py

#SPAdes genome assembler v4.0.0
export PATH=/opt/conda/bin/:$PATH && spades.py

# megahit: MEGAHIT v1.2.9
export PATH=/opt/conda/bin/:$PATH && megahit

# freebayes  version:  v1.3.7
/opt/conda/bin/freebayes

# minimap2 2.28-r1209
/opt/conda/bin/minimap2

# iVar version 1.3.2
/opt/conda/bin/ivar

# PRINSEQ-lite 0.20.4
export PATH=/opt/conda/bin/:$PATH && prinseq-lite.pl

# megan 6.25.9
/opt/conda/bin/blast2lca

# ResFinder 4.5.0
export PATH=/opt/conda/bin/:$PATH && python3 -m resfinder

# bbmap
/opt/conda/bin/bbmap.sh

# fastqtk Version: 0.27
/opt/conda/bin/fastqtk

# krona
/opt/conda/bin/ktImportKrona

# covtobed 1.3.5
/opt/conda/bin/covtobed

# MultiQC v1.23
/opt/conda/bin/multiqc

# MAFFT v7.526
/opt/conda/bin/mafft

# Prokka 1.14.6
export PATH=/opt/conda/bin/:$PATH && prokka