seqtk utils using klib
C Objective-C
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seqtk_sdust
README.md
seqtk_concat
seqtk_counts
seqtk_deinterleave
seqtk_demultiplex
seqtk_freq
seqtk_interleave
seqtk_names
seqtk_split
seqtk_subseq
seqtk_tab

README.md

seqtk_sdust

1 comile

gcc -O2 -D_NO_NT4_TBL seqtk_sdust.c sdust.c -o seqtk_sdust -lz kalloc.c

2 interface

$ seqtk_sdust
    Usage: seqtk_sdust [-p 2.0] [-w 64] [-t 20] <in.fa>
    Options:
      -c FLOAT  coverage cutoff for different contigs/reads to filter, defalut [2.0]
      -w INT    window size W, defalut [64]
      -t INT    score threshold T, defalut [20]
      -v        print version number

source code sdust.h sdust.c from: https://github.com/lh3/minimap2

3 example

seqtk_sdust -c 0.9 -w 20 -t 20 test.fasta >/dev/null

Mask the low complexity regin in the fasta sequence and filter the sequence with -c option.