seqtk '$output1' ]]>

| 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}, }