seqtk
'$output1'
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Options: -q INT mask bases with quality lower than INT [0]
-X INT mask bases with quality higher than INT [255]
-n CHAR masked bases converted to CHAR; 0 for lowercase [0]
-l INT number of residues per line; 0 for 2^32-1 [0]
-Q INT quality shift: ASCII-INT gives base quality [33]
-s INT random seed (effective with -f) [11]
-f FLOAT sample FLOAT fraction of sequences [1]
-M FILE mask regions in BED or name list FILE [null]
-L INT drop sequences with length shorter than INT [0]
-c mask complement region (effective with -M)
-r reverse complement
-A force FASTA output (discard quality)
-C drop comments at the header lines
-N drop sequences containing ambiguous bases
-1 output the 2n-1 reads only
-2 output the 2n reads only
-V shift quality by '(-Q) - 33'
-U convert all bases to uppercases
-S strip of white spaces in sequences
]]>
@misc{githubseqtk,
author = {LastTODO, FirstTODO},
year = {TODO},
title = {seqtk},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/lh3/seqtk},
}