---
name: "yanagiba"
section: "1"
platform: "linux"
package: "yanagiba"
version: "1.0.0-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/yanagiba"
---

# yanagiba(1)

Filters low quality Oxford Nanopore reads basecalled with Albacore

## NAME

yanagiba - Filters low quality Oxford Nanopore reads basecalled with Albacore

## DESCRIPTION

usage: yanagiba \[-h\] **-i** INFILE \[-s SUMMARYFILE\] \[-o OUTFILE\] \[-l MINLEN\]

-

  \[-q MINQUAL\] \[--headtrim HEADTRIM\] \[--tailtrim TAILTRIM\] \[-u\]

Filter and slice Nanopore reads which have been basecalled with Albacore. Takes fastq.gz and an Albacore summary file.

### optional arguments:

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

  show this help message and exit

- **-i** INFILE, **--infile** INFILE

  Input fastq.gz file.

- **-s** SUMMARYFILE, **--summaryfile** SUMMARYFILE

  Albacore summary file with header row.

- **-o** OUTFILE, **--outfile** OUTFILE

  Write filtered reads to this file in .bgz format.

- **-l** MINLEN, **--minlen** MINLEN

  Exclude reads shorter than this length. Default: 0

- **-q** MINQUAL, **--minqual** MINQUAL

  Minimum quality score to retain a read. Default: 10

- **--headtrim** HEADTRIM

  Trim x bases from beginning of each read. Default: 0

- **--tailtrim** TAILTRIM

  Trim x bases from end of each read. Default: None

- **-u**, **--forceunique**

  Enforce unique reads. Only store first instance of a read from fastq input where readID occurs multiple times.

## AUTHOR

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