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fulcrumgenomics / stitch

Stitch is a toolkit for analysis of chimeric reads in sequencing data
MIT License
9 stars 3 forks source link

Support input of reads in FASTA #39

Closed jdidion closed 1 year ago

nh13 commented 1 year ago

Shall we also add support of other common formats?
E.g. GenBank (.gb) which are frequently output as part of assemblies from plasmid/vector sequencing providers

Or should we link to toolkits that can do that conversion for us? And if they don't exist, add a conversion tool in this toolkit?

jdidion commented 1 year ago

Converting genbank to other formats seems like something I'd put in a stand-alone library, or one with similar functions. Then we could decide whether to wrap it in a stand-alone tool or make it a dependency of stitch to directly support genbank input.

Another idea is directly pulling from SRA/ENA via an accession.

nh13 commented 1 year ago

Why not have a toolkit "2fq" that converts input formats to FASTQ

jdidion commented 1 year ago

I need a toolkit to manage the list of toolkits I have (and want to write)