Command line Programs

fast5_research comes with two commandline programs for conversion of sequencing read data.

extract_reads - extracts reads from a bulk .fast5 to either single- or multi-read .fast5:

usage: extract_reads [-h] [--multi | --single] [--flat] [--by_id]
                     [--prefix PREFIX]
                     [--channel_range CHANNEL_RANGE CHANNEL_RANGE]
                     [--workers WORKERS] [--limit LIMIT]
                     input output

Bulk .fast5 to read .fast5 conversion.

positional arguments:
  input                 Bulk .fast5 file for input.
  output                Output folder.

optional arguments:
  -h, --help            show this help message and exit
  --multi               Output multi-read files.
  --single              Output single-read files.
  --flat                Create all .fast5 files in one directory
  --by_id               Name single-read .fast5 files by read_id.
  --prefix PREFIX       Read file prefix.
  --channel_range CHANNEL_RANGE CHANNEL_RANGE
                        Channel range (inclusive).
  --workers WORKERS     Number of worker processes.
  --limit LIMIT         Limit reads per channel.

filter_reads - extracts a subset of reads from a set of multi-read .fast5 files.

usage: filter_reads [-h] [--tsv_field TSV_FIELD] [--multi | --single]
                    [--prefix PREFIX] [--recursive] [--workers WORKERS]
                    input output filter

Extract reads from multi-read .fast5 files.

positional arguments:
  input                 Path to input multi-read .fast5 files.
  output                Output folder.
  filter                A .tsv file with column `read_id` defining required
                        reads.

optional arguments:
  -h, --help            show this help message and exit
  --tsv_field TSV_FIELD
                        Field name from `filter` file to obtain read IDs.
  --multi               Output multi-read files.
  --single              Output single-read files.
  --prefix PREFIX       Read file prefix.
  --recursive           Search recursively under `input` for source files.
  --workers WORKERS     Number of worker processes.