---
name: "catfishq"
section: "1"
platform: "linux"
package: "catfishq"
version: "1.4.0+ds-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/catfishq"
---

# catfishq(1)

concatenates fastq files

## NAME

catfishq - concatenates fastq files

## DESCRIPTION

usage: catfishq \[-h\]

-

  \[--log {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical}\] \[-o OUT\] \[-l MIN\_LEN\] \[-q MIN\_QSCORE\] \[--max-sequencing-time MAX\_SEQ\_TIME\] \[--min-sequencing-time MIN\_SEQ\_TIME\] \[--start-time START\_TIME\] \[--print-start-time\] \[-n MAX\_N\] \[-b MAX\_BP\] \[-r\] \[-d\] FASTQ \[FASTQ ...\]

Cat long lists of FASTQ files

### positional arguments:

- FASTQ

  FASTQ files or folders containing FASTQ files

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **--log** {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical}

  Print debug information

- **-o** OUT, **--output** OUT

  Output file. (default: stdout)

- **-l** MIN\_LEN, **--min-length** MIN\_LEN

  Minimum read length

- **-q** MIN\_QSCORE, **--min-qscore** MIN\_QSCORE

  Minimum q-score

- **--max-sequencing-time** MAX\_SEQ\_TIME

  Only output reads that where sequenced up to the given time (minutes).

- **--min-sequencing-time** MIN\_SEQ\_TIME

  Only output reads that where sequenced after the given time (minutes).

- **--start-time** START\_TIME

  Starttime of the run as guppy time stamp (only required with **--sequencing-time**). If 'min' is given as argument the minimal time is detected automatically.

- **--print-start-time**

  Print the minimal start\_time of all fastq files

- **-n** MAX\_N, **--max\_n** MAX\_N

  Stop after \<max\_n\> reads

- **-b** MAX\_BP, **--max\_mbp** MAX\_BP

  Stop after \<max\_bp\> mega base pairs

- **-r**, **--recursive**

  Search folders recursively

- **-d**, **--dedup**

  Remove duplicated reads.

## AUTHOR

 This manpage was written by Steffen Moeller for the Debian distribution and\
  can be used for any other usage of the program.