README.md

Nx

Contig statistic (N50, L50, ........) for .fastq files (gz and bz2 compresions are supported).

Designed for large data.

Build

1. Clone this repository
2. Install rust language
3. Install cargo package manager
4. Build the project

cargo build --release

The binary is located at target/release/nx

Usage

nx BUCKET_COUNT GLOB_PATTERN [*glob_pattern2]

• BUCKET_COUNT
  • number of bucket
  • e.g. 2 calculate N50, L50
  • e.g. 3 calculate N33, N66, L33, L66
• GLOB_PATTERN
  • pattern for .fastq, .fastq.gz or .fastq.buz2 files
  • or files itself

Examples

Calculate N50 from all .fastq files

nx 2 data/*.fastq

Calculate N10 .. N90 from .gz files

nx 10 data/data1.fastq.gz data/data2.fastq.gz