https://github.com/andreaguarracino/chain2paf
convert CHAIN format to PAF format
https://github.com/andreaguarracino/chain2paf
Last synced: 2 months ago
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convert CHAIN format to PAF format
- Host: GitHub
- URL: https://github.com/andreaguarracino/chain2paf
- Owner: AndreaGuarracino
- License: mit
- Created: 2022-02-12T13:10:18.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2024-12-17T15:03:03.000Z (6 months ago)
- Last Synced: 2025-03-24T19:45:10.391Z (3 months ago)
- Language: Rust
- Size: 156 KB
- Stars: 14
- Watchers: 3
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# chain2paf
convert CHAIN format to PAF format
## citation
[](https://doi.org/10.5281/zenodo.8108426)
## installation
`chain2paf` is built with rust, and so we install using `cargo`:
```shell
git clone https://github.com/AndreaGuarracino/chain2paf
cd chain2paf
cargo install --force --path .
```
## usage
With alignments in `data/hg18ToHg19.over.chain`, we would convert it into a PAF format file using this call:
```shell
chain2paf -i data/hg18ToHg19.over.chain > hg18ToHg19.over.chain.paf
```
If full CIGAR strings (with `=`/`X` operators) are required, we can specify two FASTA files (uncompressed or bgzipped),
the 1-st for the targets and the 2-nd for the queries. For example, if the sequences of the human genome versions
hg18 and hg19 are available in the `hg18.fa.gz` and `hg19.fa.gz` files, you can execute
```shell
chain2paf -i data/hg18ToHg19.over.chain -f hg18.fa.gz hg19.fa.gz > hg18ToHg19.over.chain.paf
```
If the CHAIN file is the result of a pairwise alignment, you can specify the same FASTA file for both targets and queries:
```shell
chain2paf -i input.chain -f input.fa.gz input.fa.gz > input.chain.paf
```
## info
`chain2paf` performs the reverse operation of [paf2chain](https://github.com/AndreaGuarracino/paf2chain).