I have figured out the organisms that need to be filtered out from the samples with the help of CCMetagen taxonomical classification tool. By using the taxid(s) that were generated by the CCMetagen as output, I located the refseq(s) from the NCBI database. When I downloaded the zip file, I came to know there are a lot of sequenced nucleotide files with .fna extension inside one zip file such as unplaced.scaf.fna and chrPltd.fna. Now, I am confused about which sequenced nucleotide files do have to use by me as a reference to do the mapping using Bowtie2?
1 answer
We prepared a curated metagenomic infput file of all finished bacteria and provide it in the owncloud link in this repo: https://github.com/MHH-RCUG/Wochenende
You can build a bwa mem or bowtie2 index from one of those fastas, i.e. the most recent.
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