fu-index

Extracts the index (barcode) from Illumina demultiplexed files.

Fastx utility  A program to print the Illumina INDEX of a set of FASTQ files  Usage:   fu-index [options] <FASTQ>...  Options:      -m, --max-reads INT    Evaluate INT number of reads, 0 for unlimited [default: 8000]    -r, --min-ratio FLOAT  Minimum ratio of matches of the top index [default: 0.90]    -h, --header           Add header to output    --verbose              Print verbose log    --help                 Show help

Input files

FASTQ files demultiplexed by CASAVA (Illumina).

Example output

A tabular output contains:

  • filename
  • extracted tag
  • fraction of the top tag (accounts for errors)
  • PASS ("PASS" or "–") if the top tags is >= min-ratio
  • Instrument code (from 1.12)
  • Run number (from 1.12)
  • Flowcell ID (from 1.12)
data/illumina_1.fq.gz   TACGCTGC+CTATTAAG       1.00    PASS    A00709  43      HYG25DSXXdata/illumina_2.fq.gz   TACGCTGC+CTATTAAG       1.00    PASS    A00709  43      HYG25DSXX