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.