How to convert .sra to .fa instead of .fastq?
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6.7 years ago
vassialk ▴ 200

How to convert .sra to .fa instead of .fastq? That is an input requirements for the BBMap. Thx.

sequencing wgs software error • 1.7k views
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With a little search on google I guess you can find the solution... have you tried it?

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BBMap includes reformat.sh which can convert between fasta and fastq. That said - sra archives are generally for reads, which should be kept in fastq format. There's nothing in the BBMap package that requires fasta instead of fastq with the exception of the reference input for BBMap, and you should not be mapping using short reads as a reference.

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6.7 years ago

Are you using the SRA toolkit from NCBI? If so, see the fastq-dump guide here.

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