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seqtk_seq (version 1.4+galaxy1)

Input FASTA/Q file:

Mask bases with quality lower than INT:

Mask bases with quality higher than INT:

Masked bases converted to CHAR; leave empty for lowercase masking:

Number of residues per line; 0 for 2^32-1:

Quality shift: ASCII-INT gives base quality:

Only applied during comparison to quality thresholds for masking

Random seed:

Effective with -f

Sample fraction of sequences:

Mask regions in BED or name list file:

Drop sequences with length shorter than INT:

Mask complement region:

Effective with -M

Reverse complement:

Force FASTA output (discard quality):

Drop comments at the header lines:

Drop sequences containing ambiguous bases:

Output the 2n-1 reads only:

Output the 2n reads only:

What it does

Various utilities for transforming FASTA/Q data

Attribution

This Galaxy tool relies on the seqtk toolkit from lh3/seqtk, developed by Heng Li at the Broad Institute