How to get both reads (in paired end read uploads) that map to a taxon
Currently, if you download the reads that map to a taxon, if you uploaded paired-end reads and only one out of the two mapped to that taxon, the downloaded file only contains the read that mapped and omits the other half of the pair.
If you are interested in getting both reads (e.g. to do de novo assembly), you can do the following:
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Download the reads for the taxon (by hovering over the taxon in the report table and clicking the download link)
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Download all the non-host reads for the sample (by navigating to the details page and clicking on "Non-Host Reads")
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Download this python script and run it on the two files:
./AllReads.py sample_pseudomonas-hits.fasta sample_nonhost.fasta