Yet Another Chimeric Read Detector for long reads

Using all-against-all read mapping, yacrd performs:

1. computation of pile-up coverage for each read
2. detection of chimeras

Chimera detection is done as follows:

1. for each region where coverage is smaller or equal than min_coverage (default 0), yacrd creates a gap.
2. if there is a gap that starts at a position strictly after the beginning of the read and ends strictly before the end of the read, the read is marked as Chimeric
3. if gaps length of extremity > 0.8 * read length, the read is marked as Not_covered

Rationale

Long read error-correction tools usually detect and also remove chimeras. But it is difficult to isolate or retrieve information from just this step.

DAStrim (from the DASCRUBBER suite does a similar job to yacrd but relies on a different mapping step, and uses different (likely more advanced) heuristics. Yacrd is simpler and easier to use.

This repository contains a set of scripts to evaluate yacrd against other similar tools such as DASCRUBBER and miniscrub on real data sets.

Input

Any set of long reads (PacBio, Nanopore, anything that can be given to minimap2). yacrd takes the resulting PAF (Pairwise Alignement Format) from minimap2 or BLASR m4 file from some other long reads overlapper as input.

Requirements

• Rust in stable channel
• libgz
• libbzip2
• liblzma

Instalation

With cargo

If you have a rust environment setup you can run :

cargo install yacrd

With conda

yacrd is avaible in bioconda channel

if bioconda channel is setup you can run :

conda install yacrd

From source

git clone https://github.com/natir/yacrd.git
cd yacrd
git checkout v0.5.1

cargo build
cargo test
cargo install

How to use Yacrd

Find chimera

minimap2 reads.fq reads.fq | yacrd -o reads.yacrd

If you want save mapping intermediate file:

minimap2 reads.fq reads.fq > mapping.paf
yacrd chimeric -i mapping.paf -o reads.yacrd

Find chimera and run post-detection operation

yacrd can perform thrid post-detection operation, on mapping or sequence file:

• filtering: yacrd generate a new file with only record without chimeric reads
• extracting: yacrd generate a new file with only record with chimeric reads
• spliting (only on sequence file) : yacrd generate a new file without chimeric region

minimap2 reads.fq reads.fq > mapping.paf
yacrd chimeric -i mapping.paf -f reads.fasta > reads.yacrd # produce reads_fileterd.fasta
yacrd chimeric -i mapping.paf -e reads.fasta > reads.yacrd # produce reads_extracted.fasta
yacrd chimeric -i mapping.paf -s reads.fasta > reads.yacrd # produce reads_splited.fasta

Read scrubbing

yacrd support a scrubbing mode to remove all not supported part of read.

For nanopore data, we recommand to use minimap2 with all-vs-all nanopore preset with maximal distance between seeds fixe to 500 (option -g 500) to generate overlap. We recommand to run yacrd with minimal coverage fixed to 4 (option -c) and minimal coverage of read fixed to 0.4 (option -n).

This is an exemple of how run a yacrd scrubbing:

minimap2 -x ava-ont -g 500 reads.fasta reads.fasta > overlap.paf
yacrd scrubbing -c 4 -n 0.4 -m overlap.paf -s reads.fasta -S reads_scrubbed.fasta -r scrubbed_report.yacrd

For pacbio P6-C4 data, we recommand to use minimap2 with all-vs-all pacbio preset with maximal distance between seeds fixe to 800 (option -g 800) to generate overlap. We recommand to run yacrd with minimal coverage fixed to 4 (option -c 4) and minimal coverage of read fixed to 0.4 (option -n 0.4).

minimap2 -x ava-pb -g 800 reads.fasta reads.fasta > overlap.paf
yacrd scrubbing -c 4 -n 0.4 -m overlap.paf -s reads.fasta -S reads_scrubbed.fasta -r scrubbed_report.yacrd

For pacbio Sequel data, we recommand to use minimap2 with all-vs-all pacbio preset with maximal distance between seeds fixe to 5000 (option -g 5000) to generate overlap. We recommand to run yacrd with minimal coverage fixed to 3 (option -c 3) and minimal coverage of read fixed to 0.4 (option -n 0.4).

minimap2 -x ava-pb -g 5000 reads.fasta reads.fasta > overlap.paf
yacrd scrubbing -c 3 -n 0.4 -m overlap.paf -s reads.fasta -S reads_scrubbed.fasta -r scrubbed_report.yacrd

Output

type_of_read	id_in_mapping_file  length_of_read  length_of_gap,begin_pos_of_gap,end_pos_of_gap;length_of_gap,be…

Example

Not_covered readA 4599	3782,0,3782

Here, readA doesn't have sufficient coverage, there is a zero-coverage region of length 3782bp between positions 0 and 3782.

Chimeric    readB   10452   862,1260,2122;3209,4319,7528

Here, readB is chimeric with 2 zero-coverage regions: one between bases 1260 and 2122, another between 3209 and 7528.

JSON

If flag -j are present output are write in json format, an example:

{
	"1": {
		"gaps": [{
			"begin": 0,
			"end": 2000
		}, {
			"begin": 4500,
			"end": 5500
		}, {
			"begin": 8000,
			"end": 10000
		}],
		"length": 10000,
		"type": "Chimeric"
	},
	"4": {
		"gaps": [{
			"begin": 2500,
			"end": 3500
		}],
		"length": 6000,
		"type": "Chimeric"
	}
}

Citation

If you use yacrd in your research, please cite the following publication:

Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré, yacrd and fpa: upstream tools for long-read genome assembly

bibtex format:

@article {Marijon2019,
	author = {Marijon, Pierre and Chikhi, Rayan and Varr{\'e}, Jean-St{\'e}phane},
	title = {yacrd and fpa: upstream tools for long-read genome assembly},
	elocation-id = {674036},
	year = {2019},
	doi = {10.1101/674036},
	URL = {https://www.biorxiv.org/content/early/2019/06/18/674036},
	eprint = {https://www.biorxiv.org/content/early/2019/06/18/674036.full.pdf},
	journal = {bioRxiv}
}