---
name: "Fast5_to_seq_summary"
section: "1"
platform: "linux"
package: "pycoqc"
version: "2.5.2+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Fast5_to_seq_summary"
---

# Fast5\_to\_seq\_summary(1)

generate a sequencing summary like file from a directory containing Fast5 files

## NAME

Fast5\_to\_seq\_summary - generate a sequencing summary like file from a directory containing Fast5 files

## DESCRIPTION

usage: Fast5\_to\_seq\_summary \[-h\] \[--version\] **--fast5\_dir** FAST5\_DIR

- **--seq\_summary\_fn** SEQ\_SUMMARY\_FN

  \[--max\_fast5 MAX\_FAST5\] \[--threads THREADS\] \[--basecall\_id BASECALL\_ID\] \[--fields FIELDS \[FIELDS ...\]\] \[--include\_path\] \[--verbose\_level VERBOSE\_LEVEL\]

Fast5\_to\_seq\_summary generate a sequencing summary like file from a directory containing Fast5 files

### optional arguments:

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

  show this help message and exit

- **--version**, **-v**

  show program's version number and exit

- **--fast5\_dir** FAST5\_DIR, **-f** FAST5\_DIR

  Directory containing fast5 files. Can contain multiple subdirectories

- **--seq\_summary\_fn** SEQ\_SUMMARY\_FN, **-s** SEQ\_SUMMARY\_FN

  path of the summary sequencing file where to write the data extracted from the fast5 files

- **--max\_fast5** MAX\_FAST5

  Maximum number of file to try to parse. 0 to deactivate (default: 0)

- **--threads** THREADS, **-t** THREADS

  Total number of threads to use. 1 thread is used for the reader and 1 for the writer. Minimum 3 (default: 4)

- **--basecall\_id** BASECALL\_ID

  id of the basecalling group. By default leave to 0, but if you perfome multiple basecalling on the same fast5 files, this can be used to indicate the corresponding group (1, 2 ...) (default: 0)

- **--fields** FIELDS \[FIELDS ...\]

  list of field names corresponding to attributes to try to fetch from the fast5 files (default: \['read\_id', 'run\_id', 'channel', 'start\_time', 'sequence\_length\_template', 'mean\_qscore\_template', 'calibration\_strand\_genome\_template', 'barcode\_arrangement'\])

- **--include\_path**

  If given, the absolute path to the corresponding file is added in an extra column (default: False)

- **--verbose\_level** VERBOSE\_LEVEL

  Level of verbosity, from 2 (Chatty) to 0 (Nothing) (default: 0)

## AUTHOR

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