Nikos Tsardakas RenhuldtApr 24, 2024
I want to produce a #gff of #kmer positions in a #genome. I'm only looking for exact matches, which should make this computationally straight forward. What tools do y'all use for this? Previously I've used GMAP, but it feels like that should be overkill for this very minor task (essentially a grep but with GFF output). #SeqKit locate ends up consuming a lot of memory, but maybe I'm invoking it wrong?
Christos Argyropoulos MD, PhDSep 16, 2023

Creating #fastq #parsers in #perl and comparisons against the CLI #seqtk (C) #seqkit(#golang).

A. Statement of the problem:

https://blogs.perl.org/users/chrisarg/2023/09/of-go-c-perl-and-fastq-file-conversion-vol-i-intro.html

B. Regex based parser:

https://blogs.perl.org/users/chrisarg/2023/09/of-go-c-perl-and-fastq-file-conversion-vol-ii-the-jedi-regex.html

C. Converting the Regex parser into fast & tedious flag based code:

https://blogs.perl.org/users/chrisarg/2023/09/of-go-c-perl-and-fastq-file-conversion-vol-iii-pledging-allegiance-to-the-flag.html

D. Speed comparisons:

https://blogs.perl.org/users/chrisarg/2023/09/of-go-c-perl-and-fastq-file-conversion-vol-iv-gone-in-60-seconds-or-less.html

The interpreted (flag based) #perl gets within 7% of the compiled #clang parser. Both perl parsers have highly stable performance (decreased variability)

Of Go, C, Perl and fastq file conversion Vol I : intro | chrisarg [blogs.perl.org]