Will Kallisto or Salmon perform streaming alignment from the Sequence Read Archive?
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3.8 years ago
b10hazard ▴ 30

Do either Kallisto or Salmon have the ability to align data streamed from the Sequence Read Archive (SRA). Like what HISAT2 can do with the --sra-acc option?

Thanks!

kallisto salmon pseudoaligners • 1.0k views
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You can see an example of a snakemake script to do this with kallisto here: [https://github.com/pachterlab/bears_analyses] Not streaming but could be modified to do so.

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There is a blogpost describing how to do this for single-cell RNA-seq here: https://sinabooeshaghi.com/2019/07/09/fasterq-to-count-matrices-for-single-cell-rna-seq/

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3.8 years ago
Rob 5.3k

There is no option in salmon directly equivalent to the --sra-acc option in HISAT. However, salmon will happily accept streaming input from a fifo or named pipe. Hence, it should be possible to create a bash / snakemake / nextflow script to do the conversion and feeding of the reads directly to salmon so that you don't have to have the intermediate files sitting on your disk.

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Thank you for the suggestion. I will give that a shot.