fastqutils / filter

Filter reads in a FASTQ file. The filtering criteria can be applied as a
batch, allowing you to use more than one criterion at a time.

Usage: fastqutils filter {opts} {filters} file.fastq{.gz}
  -discard filename           Write the name of all discarded reads to a file
  -illumina                   Use Illumina scaling for quality values
                              (-qual filter) [default: Sanger-scale]
  -stats filename             Write filter stats out to a file
  -v                          Verbose

  -wildcard num               Discard reads w/ more than N wildcards (N or .)

  -size minsize               Discard reads that are too short

  -truncate size              Trim reads to a maximum length

  -qual minval window_size    Truncate reads (5'->3') where the quality falls
                              below a threshold (floating average over

  -prefix size                Trim away [size] bases from the 5' end

  -suffixqual minval          Trim away bases from the 3' end with low quality
                              value should be given as a character (in Sanger
                              scale)(like Illumina B-trim)

  -trim seq pct mintrim       Trim away at least [mintrim] bases that match a
                              [sequence] (3' adaptor) allowing for a match
                              percentage [pct] (0.0-1.0)

  -paired                     Only keep reads that are correctly paired
                              (Requires an interleaved FASTQ file)

  -whitelist keeplist.txt     Only keep reads whose name is in the keeplist