https://github.com/andreaguarracino/paf2chain

convert PAF format to CHAIN format
https://github.com/andreaguarracino/paf2chain

Last synced: about 2 months ago
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convert PAF format to CHAIN format

• Host: GitHub
• URL: https://github.com/andreaguarracino/paf2chain
• Owner: AndreaGuarracino
• License: mit
• Created: 2021-08-07T05:48:57.000Z (almost 4 years ago)
• Default Branch: master
• Last Pushed: 2024-12-16T15:38:54.000Z (6 months ago)
• Last Synced: 2025-04-10T22:45:25.800Z (about 2 months ago)
• Language: Rust
• Size: 24.4 KB
• Stars: 28
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# paf2chain

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/paf2chain/README.html)

convert PAF format to CHAIN format

## citation

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8108447.svg)](https://doi.org/10.5281/zenodo.8108447)

## installation

`paf2chain` is built with rust, and so we install using `cargo`:

```

git clone https://github.com/AndreaGuarracino/paf2chain

cd paf2chain

cargo install --force --path .

```

## usage

Generate alignments with the cigar string attached to the `cg:Z:` tag.

These can be made by several aligners, including `minimap2 -c`, `wfmash`, or `lastz --format=paf:wfmash`.

With alignments in `aln.paf` (or `aln.paf.gz` if gzip-compressed), we would convert it into a CHAIN format file using this call:

```

paf2chain -i aln.paf > aln.chain

```

## info

`paf2chain` performs the reverse operation of [chain2paf](https://github.com/AndreaGuarracino/chain2paf).