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.

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 MHAP 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 v0.5.0

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 -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

Scrubber read

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

minimap2 reads.fq reads.fq > mapping.paf
yacrd scrubbing -m mapping.paf -s reads.fq -S reads_scrubbed.fq -r report.yacrd
yacrd scrubbing -m mapping.paf -s reads.fq -S reads_scrubbed.fq -r report.yacrd -c 10 # Remove part not covered by 10 reads
yacrd scrubbing -m mapping.paf -s reads.fq -S reads_scrubbed.fq -j -r report.yacrd.json

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"
	}
}