https://github.com/sandyjmacdonald/fast_stats_julia

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

Last synced: about 2 months ago
JSON representation

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_julia
• Owner: sandyjmacdonald
• License: mit
• Created: 2014-11-05T21:46:37.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2015-07-20T16:57:52.000Z (over 9 years ago)
• Last Synced: 2024-04-21T04:04:57.954Z (9 months ago)
• Language: Julia
• Homepage:
• Size: 137 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
fast_stats.jl

===========

Returns N50 (or N of your choice) and other stats of a fasta/q 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.

Runs significantly faster for large numbers of sequences than the Python version.

For example, this Julia version ran through 5,000,000 250 base pair sequences

(gzipped fastq) in 28.65 seconds compared to 6 minutes 44.55 seconds for the

Python version.

### Dependencies

Requires the [ArgParse](http://docs.julialang.org/en/release-0.1/stdlib/argparse/)

module for parsing the command line arguments, and the

[GZip](https://github.com/JuliaLang/GZip.jl) module for reading gzipped input.

You can install these by opening an interactive Julia prompt and typing:

	Pkg.add("ArgParse")

	Pkg.add("GZip")

### Usage

    julia fast_stats.jl --in  --n 50

> ##### Arguments

> `--in` 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.