Randomly subsample sequencing reads or alignments
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Published by mbhall88 6 months ago
reads
subcommandcite
command to get citation (db17612)aln
to subsample alignments (b92979a)reads
subcommand (f48d47b)Published by mbhall88 10 months ago
Published by github-actions[bot] over 1 year ago
Published by github-actions[bot] over 2 years ago
--frac
) and number (--num
) options. This allows users to replicate theseqtk sample
[#34]Published by github-actions[bot] over 2 years ago
rasusa
as the entry command for docker container [#35]Published by github-actions[bot] about 3 years ago
--bases
option to allow for manually setting the target number of bases to keep--genome-size
can now take a FASTA/Q index file and the sum of all referencePublished by github-actions[bot] about 3 years ago
niffler
). This is either inferred from the file extension or manually via the -O
option.-l
Vec<bool>
instead of HashSet
to store the indices of reads to keep. This gives a nice little speedup (see #28), A big thank you to @natirPublished by github-actions[bot] about 3 years ago
Published by github-actions[bot] about 3 years ago
Published by github-actions[bot] about 3 years ago
snafu
and failure
for error handling to anyhow
and thiserror
. Based on the procedure outlined in this excellent blog post.Published by mbhall88 over 4 years ago
Version 0.3.0 may give different results to previous versions. If so,
the differences will likely be a handful of extra reads (possibly none).
The reason for this is --coverage
is now treated as a float.
Previously we immediately round coverage down to the nearest integer. As
the number of reads to keep is based on the target total number of
bases, which is coverage * genome size. So if coverage is 10.7 and
genome size is 100, previously our target number of bases would have
been 1000, whereas now, it would be 1070.
--coverage
is now treated as a f32
instead of being convertedrust-bio
to version 0.31.0. This means rasusa
now handlesbash
to the docker image b47a8b75943098bdd845b7758cf2eab01ef5a3d8Published by mbhall88 almost 5 years ago