https://github.com/sandyjmacdonald/fast_stats

Returns N50 (or N of your choice) and other stats of a fasta/q file of sequences.
https://github.com/sandyjmacdonald/fast_stats

Last synced: 13 days ago
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Returns N50 (or N of your choice) and other stats of a fasta/q file of sequences.

• Host: GitHub
• URL: https://github.com/sandyjmacdonald/fast_stats
• Owner: sandyjmacdonald
• License: mit
• Created: 2014-08-29T16:16:13.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2015-07-20T11:50:37.000Z (over 9 years ago)
• Last Synced: 2024-11-11T09:18:01.971Z (2 months ago)
• Language: Python
• Homepage:
• Size: 156 KB
• Stars: 3
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
fast_stats.py

===========

Returns N50 (or N of your choice) and other stats of a fasta/fastq file (can be

gzipped) of sequences. N50 is calculated as the sequence length above which 50%

of the total sequence length lies when the sequences are sorted in order of

descending length.

### Dependencies

Requires [Numpy](http://www.numpy.org) for calculating the median read length.

### Usage

    python fast_stats.py -i  -n 50

> ##### Arguments

> `-i` The fasta/q file (can be gzipped) for which you want to calculate the stats.

> `-n` The value of n (usually 50) that you want to use.

> `-h` Displays help.