Commit 38f15a9e authored by Alexis  CRISCUOLO's avatar Alexis CRISCUOLO

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# contig_info
_contig_info_ is a command line program written in [Bash](https://www.gnu.org/software/bash/) that allows estimating several standard descriptive statistics (e.g. residue counts, sequence lengths, [N50](https://www.nature.com/articles/35057062), [NG50](https://genome.cshlp.org/content/21/12/2224), ...) from a FASTA-formatted contig file.
## Installation and execution
Give the execute permission to the file `contig_info.sh` by typing:
```bash
chmod +x contig_info.sh
```
and launch it with the following command line model:
```bash
./contig_info.sh [options]
```
## Usage
Launch _contig_info_ without option to read the following documentation:
```
USAGE: contig_info.sh [options] <contig_file>
where 'options' are:
-m <int> minimum contig length; every contig sequence of length
shorter than this cutoff will be discarded (default: 0)
-g <int> expected genome size for computing NG50, NG75 and NG90
values instead of N50, N75 and N90 ones, respectively
-d print contig sequence length distribution
-l print length of each contig sequence
-r print residue counts
-t tab-delimited output
```
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