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Alternatives to FASTQ/A Collapser of FASTX-Toolkit

Hi All,

I am trying to analyze nextgen seguencing data with Biopython (on a Windows computer). My data has certain sequences that appear many times. I was wondering how I can count the repeats and at the same remove these repeats. At the end, I would like a fasta file with a read number beside every unique sequence. My understanding is that the FASTQ/A collapser of the FASTX-toolkit will do exactly what I would like. However, I would much prefer to be able to do it on my computer without dealing with something like Linux or uploading my data to Galaxy. Any tips or suggestions on how I can do this in Biopython or anything else that I can readily use on my computer would be greatly appreciated.

Thank you very much!

sequencing analysis
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updated by GenoMax GenoMax • written by clam • clam

1 answer

You need clumpify.sh from BBMap. It is Java so will even work on Windows. But be aware that you may need good bit of RAM available depending on amount of data you have.

Be sure to check both posts by author of BBMap @Brian in this thread (Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates. ).

Once you have collapsed the fastq files you can then convert them to fasta format by using another member of BBMap suite as follows:

reformat.sh in=your_file.fq out=your_file.fa
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written by GenoMax GenoMax

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