Mapping SRA files without unpacking?

Mapping SRA files without unpacking?

1

Hi,
Is it possible to submit SRA files for alignment directly to short read aligners like Bowtie, avoiding the intermediate step of unpacking data to fastq?
Thanks!


alignment


Bowtie


SRA


sequencing

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As of version 2.3.5 bowtie2 now supports aligning SRA reads.
Prepackaged builds will include a package that supports SRA.

Use as follows

bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | b <bam>} -S [<sam>]

bowtie v.1x does not support input of SRA accessions.


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