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https://github.com/lh3/miniprot

Align proteins to genomes with splicing and frameshift
https://github.com/lh3/miniprot

bioinformatics sequence-alignment

Last synced: 7 days ago
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Align proteins to genomes with splicing and frameshift

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README 

        
[![Release](https://img.shields.io/github/v/release/lh3/miniprot)](https://github.com/lh3/miniprot/releases)

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## Getting Started

```sh

# download and compile

git clone https://github.com/lh3/miniprot

cd miniprot && make



# test file

./miniprot test/DPP3-hs.gen.fa.gz test/DPP3-mm.pep.fa.gz > aln.paf        # PAF output

./miniprot --gff test/DPP3-hs.gen.fa.gz test/DPP3-mm.pep.fa.gz > aln.gff  # GFF3+PAF output



# general command line: index and align in one go (-I sets max intron size based on genome size)

./miniprot -Iut16 --gff genome.fna protein.faa > aln.gff



# general command line: index first and then align (recommended)

./miniprot -t16 -d genome.mpi genome.fna

./miniprot -Iut16 --gff genome.mpi protein.faa > aln.gff



# output format

man ./miniprot.1

```



## Table of Contents



- [Getting Started](#started)

- [Introduction](#intro)

- [Users' Guide](#uguide)

  - [Installation](#install)

  - [Usage](#usage)

  - [Algorithm overview](#algo)

  - [Citing miniprot](#cite)

- [Limitations](#limit)



## Introduction



Miniprot aligns a protein sequence against a genome with affine gap penalty,

splicing and frameshift. It is primarily intended for annotating protein-coding

genes in a new species using known genes from other species. Miniprot is

similar to [GeneWise][genewise] and [Exonerate][exonerate] in functionality but

it can map proteins to whole genomes and is much faster at the residue

alignment step.



Miniprot is not optimized for mapping distant homologs because distant homologs

are less informative to gene annotations. Nonetheless, it is still possible to

tune seeding parameters to achieve higher sensitivity at the cost of

performance.



## Users' Guide



### Installation



Miniprot requires SSE2 or NEON instructions and only works on x86\_64 or ARM

CPUs. It depends on [zlib][zlib] for parsing gzip'd input files. To compile

miniprot, type `make` in the source code directory. This will produce a

standalone executable `miniprot`. This executable is all you need to invoke

miniprot.



For some unknown reason, the default gcc-4.8.5 on CentOS 7 may compile a binary

that is very slow on certain sequences but gcc-10.3.0 has more stable

performance. If possible, use a more recent gcc to compile miniprot.



### Usage



To run miniprot, use

```sh

miniprot -t8 ref-file protein.faa > output.paf

```

where `ref-file` can either be a genome in the FASTA format or a pre-built

index generated by

```sh

miniprot -t8 -d ref.mpi ref.fna

```

Because miniprot indexing is slow and memory intensive, it is recommended to

pre-build the index. FASTA input files can be optionally compressed with gzip.



Miniprot outputs alignment in the protein PAF format. Different from the more

common nucleotide PAF format, miniprot uses more CIGAR operators to encode

introns and frameshifts. Please refer to the [manpage][manpage] for detailed explanation.



For convenience, miniprot can also output GFF3 with option `--gff`:

```sh

miniprot -t8 --gff -d ref.mpi ref.fna > out.gff

```

The detailed alignment is embedded in `##PAF` lines in the GFF3 output. You can

also get detailed residue alignment with `--aln`.



If you are aligning proteins to a whole genome, it is recommended to add option

`-I` to let miniprot automatically set the maximum intron size. You can also

use `-G` to explicitly specify the max intron size.



### Algorithm overview



1. Translate the reference genome to amino acids in six phases and filter out

   ORFs shorter than 45bp. Reduce 20 amino acids to 13 distinct integers and

   extract random open syncmers of 6aa in length. By default, miniprot selects

   20% of 6-mers in average. For a reduced 6-mer at reference position `x`,

   keep the 6-mer and `floor(x/256)` in a dense hash table. This concludes the

   indexing step.



2. Given a protein sequence as query, extract 6-mer syncmers on the protein,

   look up the index for seed matches and apply minimap2-like chaining. This

   first round of chaining is approximate as the reference positions have been

   binned during indexing.



3. For each chain in step 2, redo seeding and chaining with sliding 5-mers from

   both the reference and the protein in the original chain. Miniprot uses all

   reduced 5-mers for this second round of chaining.



4. Choose top 100 (see `-N`) chains. Filter out anchors around potential

   introns or long gaps. Perform striped dynamic programming between remaining

   anchors and also extend from the first or last anchors. This gives the final

   alignment.



### Citing miniprot



If you use miniprot, please cite:



> Li, H. (2023) Protein-to-genome alignment with miniprot. *Bioinformatics*, **39**, btad014 [[PMID: 36648328]][mp-pmid].



The preprint is available at

[arXiv:2210.08052](https://arxiv.org/abs/2210.08052), which

additionally shows metrics on MetaEuk. Please note that the published paper

evaluated miniprot-0.7. The latest version may report different numbers.



## Limitations



* The initial conditions of dynamic programming are not technically correct,

  which may result in suboptimal residue alignment in rare cases.



* Support for non-splicing alignment needs to be improved.



* More manual inspection required for improved accuracy. For example, tandem

  copies in segmental duplications could be handled more carefully.



[exonerate]: https://pubmed.ncbi.nlm.nih.gov/15713233/

[genewise]: https://pubmed.ncbi.nlm.nih.gov/15123596/

[mp-pmid]: https://pubmed.ncbi.nlm.nih.gov/36648328/

[zlib]: https://zlib.net

[paftools]: https://github.com/lh3/minimap2/blob/master/misc/paftools.js

[minimap2]: https://github.com/lh3/minimap2

[spaln]: https://github.com/ogotoh/spaln

[spaln2]: https://pubmed.ncbi.nlm.nih.gov/22848105/

[manpage]: https://lh3.github.io/miniprot/miniprot.html