---
name: "gt-readjoiner-prefilter"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-readjoiner-prefilter"
---

# gt-readjoiner-prefilter(1)

Remove contained and low-quality reads and encode read set in GtEncseq format.

## NAME

gt-readjoiner-prefilter - Remove contained and low-quality reads and encode read set in GtEncseq format.

## SYNOPSIS

**gt readjoiner prefilter** \[option ...\]

## DESCRIPTION

- **-readset** \[*string*\]

  specify the readset name default: filename of first input sequence\_file

- **-db**

  specify a list of input libraries (Fasta/FastQ); for single-end libraries use the filename (which is not allowed to contain *:* symbols); for paired-end libraries with reads interleaved (f,r,f,r,...) in a single file use the notation \<filename\>:\<insertlength\>\[,\<stdev\>\] (stdev may be omitted); for paired-end with reads in two files (f, r) use the notation \<file\_f\>:\<file\_r\>:\<insertlength\>\[,\<stdev\>\]

- **-v** \[*yes\|no*\]

  be verbose (default: no)

- **-q** \[*yes\|no*\]

  suppress standard output messages (default: no)

- **-des** \[*yes\|no*\]

  store Fasta IDs (or entire descriptionsif used together with -clipdes no) warning: increases the memory requirement (default: no)

- **-clipdes** \[*yes\|no*\]

  clip Fasta descriptions after first space set to false if you need entire descriptions (default: yes)

- **-memdes** \[*yes\|no*\]

  use memory storage for descriptions (default: use temporary disk storage)

- **-maxlow** \[*value*\]

  maximal number of low-quality positions in a read default: infinite

- **-lowqual** \[*value*\]

  maximal quality for a position to be considered low-quality (default: 3)

- **-phred64** \[*yes\|no*\]

  use phred64 scores for FastQ format (default: no)

- **-help**

  display help for basic options and exit

- **-help+**

  display help for all options and exit

- **-version**

  display version information and exit

## REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.