Whole Genome Alignment Tools

A Rust library and tools for whole genome alignment files

Table of Contents

• Ciation

• Install

  • Conda
  • Build from source
  • Nix
  • Docker and Singularity

• Tools

  • Usage
  • Auto-Completion for easy-use
  • Format Conversion
  • Dotplot for MAF/PAF file
  • Extract regions from MAF file
  • View MAF file in terminal
  • Call Variants from MAF file
  • Chunk MAF file by length
  • Statistics for MAF/PAF file
  • Validate and fix PAF file
  • Filter records for MAF/PAF file
  • Rename MAF file
  • PAF Coverage for all-to-all alignment
  • Generate pseudo MAF from all-to-all PAF

• Library

• Features

• Benchmark

• ROADMAP

• Contributing

• License

Citation

If you use wgatools in your research, please cite:

Wei W, Gui S, Yang J, Garrison E, Yan J, Liu HJ. wgatools: an ultrafast toolkit for manipulating whole genome alignments. Published online September 13, 2024. doi:10.48550/arXiv.2409.08569

Install

Conda

conda install wgatools -c bioconda

Build from source

git clone https://github.com/wjwei-handsome/wgatools.git
cd wgatools
cargo build --release

or just install from git:

cargo install --git https://github.com/wjwei-handsome/wgatools.git

Nix

A nix flake is also available. You can build from within the repo like this:

nix build .#wgatools

Or directly install from github:

nix profile install github:wjwei-handsome/wgatools

Docker and Singularity

Using nix, we can derive docker and singularity images:

nix build .#dockerImage

First, we load the docker image into the local daemon:

docker load < result

It's then possible to pack up a singularity image:

singularity build wgatools-$(git log -1 --format=%h --abbrev=8).sif docker-daemon://wgatools:latest

This can be useful when running on HPCs where it might be difficult to build wgatools.

Tools

Usage

> wgatools
wgatools -- a cross-platform and ultrafast toolkit for Whole Genome Alignment Files manipulation

Version: 0.1.0

Authors: Wenjie Wei <[email protected]>

Usage: wgatools [OPTIONS] <COMMAND>

Commands:
  maf2paf         Convert MAF format to PAF format [aliases: m2p]
  maf2chain       Convert MAF format to Chain format [aliases: m2c]
  paf2maf         Convert PAF format to MAF format [aliases: p2m]
  paf2chain       Convert PAF format to Chain format [aliases: p2c]
  chain2maf       Convert Chain format to MAF format [aliases: c2m]
  chain2paf       Convert Chain format to PAF format [aliases: c2p]
  maf-index       Build index for MAF file [aliases: mi]
  maf-ext         Extract specific region from MAF file with index [aliases: me]
  chunk           Chunk MAF file by length [aliases: ch]
  call            Call Variants from MAF file [aliases: c]
  tview           View MAF file in terminal [aliases: tv]
  stat            Statistics for Alignment file [aliases: st]
  dotplot         Plot dotplot for Alignment file [aliases: dp]
  filter          Filter records for Alignment file [aliases: fl]
  rename          Rename MAF records with prefix [aliases: rn]
  maf2sam         DEV: maf2sam [aliases: m2s]
  pafcov          Calculate coverage for PAF file [aliases: pc]
  pafpseudo       Generate pesudo-maf for divergence analysis from PAF file [aliases: pp]
  gen-completion  Generate completion script for shell [aliases: gc]
  validate        Validate and fix query&target position in PAF file by CIGAR [aliases: vf]
  help            Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help (see more with '--help')
  -V, --version  Print version

GLOBAL:
  -o, --outfile <OUTFILE>  Output file ("-" for stdout), file name ending in .gz/.bz2/.xz will be compressed automatically [default: -]
  -r, --rewrite            Bool, if rewrite output file [default: false]
  -t, --threads <THREADS>  Threads, default 1 [default: 1]
  -v, --verbose...         Logging level [-v: Info, -vv: Debug, -vvv: Trace, defalut: Warn]

Each subcommand could be used with -h or --help to get more information.

Auto-Completion for easy-use

wgatools gen-completion --shell fish > ~/.config/fish/completions/wgatools.fish

Ready to enjoy it!

Format Conversion

Three mainstream formats(PAF, MAF, CHAIN) can be converted to each other.

For example, to convert MAF to PAF:

wgatools maf2paf test.maf > test.paf

or to convert PAF to MAF:

wgatools paf2maf test.paf --target target.fa --query query.fa > test.maf

Tip

If you want to convert into MAF format, you should provide target and query genome sequence files in {.fa, .fa.gz}.

stdin and stdout are supported, so you can use pipes to chain commands together🪆:

cat test.maf | wgatools maf2paf | wgatools paf2maf -g target.fa -q query.fa > test.maf

wgatools paf2chain test.paf | wgatools chain2maf -g target.fa -q query.fa | wgatools maf2chain | wgatools chain2paf > funny.paf

Dotplot for MAF/PAF file

We provide two modes for plot, for example:

• BaseLevel

This mode can catch the alignment details in each record, such as matches, insertions and deletions. This can help us to better observe the local alignment.

wgatools dotplot -f paf test/testdotplot.paf > out.html

By default, INDELs smaller than 50bp are merged with adjacent match. You can also use the parameter -l, --length to specify the threshold.

In Interactive html, you can click on the legend to view only the types of interest, for example:

Warning

NOTE: For better interactivity, the zoom function is turned on. However, if there is too much data, the effect may be limited by your browser performance.

This simple example can be found in the test directory.

• Overview

Similar to common dotplot scripts, it will draw each align record and color it according to identity.

wgatools dotplot test.maf -m overview > overview.html

😎 For vega and DIY hackers, we also provide output in json(vega schema) and csv formats.

Extract regions from MAF file

The line of MAF file is so long that it's hard to read. You can use maf-ext to extract specific region from MAF file with index:

wgatools maf-index test.maf

wgatools maf-extract test.maf -r chr1:1-10,chr2:66-888,chr3:100-50,chr_no:1-10,x:y-z

Tip

1. Support multi-interval input, separated by commas
2. Support bed input to specify interval
3. Mismatched interval are skipped and warned

View MAF file in terminal

View the MAF file in the terminal smoothly, and you can also specify the area to view:

wgatools tview test.maf

Press ◄► to slide left and right.

Press q to exit.

Press g to bring up the navigation window, where the left side is the optional sequence name, and the right side is the optional interval of the selected sequence, you can press Tab to switch the left and right selection windows, and you can press ▲▼ to select the sequence and interval

After input a legal interval, you can Press Enter to jump to the Destination. Or press Esc to exit the navigation window.

Call Variants from MAF file

The MAF format completely records the alignment of each base, so it can be used to identify variants.

Supported explicit varaint types:

• SNP
• INS
• DEL
• INV

The default parameter does not output SNP and short INS and DEL (<50). The example is as follows:

wgatools call test/test.maf -s -l0

Output vcf:

##fileformat=VCFv4.4
##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record">
##INFO=<ID=INV_NEST,Number=1,Type=String,Description="Varations nested within inversion">
##FORMAT=<ID=QI,Number=1,Type=String,Description="Query informations">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
ref.chr8	181470034	.	TG	T	.	.	SVTYPE=DEL;SVLEN=1;END=181470035	GT:QI	1|1:query.chr8@181989530@181989530@P
ref.chr8	181470279	.	G	C	.	.	.	GT	1|1
ref.chr8	181470292	.	A	G	.	.	.	GT	1|1
ref.chr8	181470431	.	C	G	.	.	.	GT	1|1
ref.chr8	181470609	.	C	A	.	.	.	GT	1|1
ref.chr8	181470641	.	C	T	.	.	.	GT	1|1
ref.chr8	181470774	.	A	AAACCAAGA	.	.	SVTYPE=INS;SVLEN=8;END=181470774	GT:QI	1|1:query.chr8@181990269@181990277@P
ref.chr8	181470793	.	G	T	.	.	.	GT	1|1
ref.chr8	181470894	.	C	T	.	.	.	GT	1|1
ref.chr8	181470895	.	A	T	.	.	.	GT	1|1
ref.chr8	181470903	.	G	A	.	.	.	GT	1|1

Important

This function does not support the identification of chromosomal rearrangements such as DUP, as this requires the extraction of sequences for realignment.

Chunk MAF file by length

You can split a huge MAF record into multiple records by length:

wgatools chunk -l 100 test/test.maf -o chunked.maf

Statistics for MAF/PAF file

wgatools stat test.maf
wgatools stat -f paf test.paf
wgatools stat test.maf

Validate and fix PAF file

In some cases, the PAF file may be incorrect, such as the query and target postions are wrong, or CIGAR string is unmatch with sequences. You can use this command to validate and fix the PAF file:

## just validate
> wgatools validate wrong.paf

Total records: 2306
Query invalid records: 2283
Target invalid records: 80
Query invalid list:...
Target invalid list:...
## validate and fix
> wgatools validate wrong.paf -f happy.paf

Filter records for MAF/PAF file

You can filter some records by block length or query_size.

For example, to filter records that contig vs reference:

wgatools filter test.maf -q 1000000 > filt.maf

For all-to-all alignment paf file which produced by wfmash, you can filter some pairs by align-size:

wgatools filter all2all.paf -a 1000000 > filt.maf

Rename MAF file

In some practices, the chromosome name of ref and query are both called chr1, which is not easy to distinguish. You can rename the sequence name in MAF file with a prefix:

wgatools rename --prefixs REF.,QUERY. input.maf > rename.maf

PAF Coverage for all-to-all alignment

If you have alignment results for multiple genomes, you can use this command to calculate the alignment coverage on the genomes. It's optimized to use with wfmash output.

wgatools pafcov all.paf > all.cov.beds

Generate pseudo MAF from all-to-all PAF

wgatools pafpseudo -f all.fa.gz all.paf -o out_dir -t 10

Tip

Practical processes and profile can refer to this pipleline and this paper

Library

Some simple reader and iterator for PAF, MAF and Chain files:

use wgatools::parser::paf::PafReader;
use wgatools::parser::maf::MAFReader;
use wgatools::parser::chain::ChainReader;
fn main() {
    let mut mafreader = MAFReader::from_path("test.maf").unwrap();
    for record in mafreader.records() {
        let record = record.unwrap();
        println!("{:?}", record);
    }
    /// ...
}

Features

• use nom to parse CIGAR string
• use rayon to accelerate the speed of conversions
• use ratatui to visualize MAF file in terminal
• ...

Benchmark

We use the hyperfine to compare the speed of conversion between wgatools and another Rust-based tool paf2chain. The result is as follows (10 runs):

command	mean(sec)	stddev	median	user	system	min	max
wgatools p2c Zm-CML333.paf -o foo	3.69	0.36	3.71	3.46	0.14	3.25	4.09
paf2chain --input Zm-CML333.paf > bar	16.28	0.86	16.27	3.80	12.03	15.01	17.67

ROADMAP

• SAM converter
• Local improvement of alignment by re-alignment
• MAF -> GAF -> HAL
• output gvcf for variants
• call variants from PAF directly

Contributing

Feel free to dive in! Open an issue or submit PRs.

License

MIT License © WenjieWei