Gapmm2: gapped alignment using minimap2 (align transcripts to genome)

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Overview

Latest Github release Conda

gapmm2: gapped alignment using minimap2

This tool is a wrapper for minimap2 to run spliced/gapped alignment, ie aligning transcripts to a genome. You are probably saying, yes minimap2 runs this with -x splice --cs option (you are correct). However, there are instances where the terminal exons from stock minimap2 alignments are missing. This tool detects those alignments that have unaligned terminal eons and uses edlib to find the terminal exon positions. The tool then updates the PAF output file with the updated information.

Rationale

We can pull out a gene model in GFF3 format that has a short 5' terminal exon:

scaffold_9	funannotate	gene	408904	409621	.	-	.	ID=OPO1_006919;
scaffold_9	funannotate	mRNA	408904	409621	.	-	.	ID=OPO1_006919-T1;Parent=OPO1_006919;product=hypothetical protein;
scaffold_9	funannotate	exon	409609	409621	.	-	.	ID=OPO1_006919-T1.exon1;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	409320	409554	.	-	.	ID=OPO1_006919-T1.exon2;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	409090	409255	.	-	.	ID=OPO1_006919-T1.exon3;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	408904	409032	.	-	.	ID=OPO1_006919-T1.exon4;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409609	409621	.	-	0	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409320	409554	.	-	2	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409090	409255	.	-	1	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	408904	409032	.	-	0	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;

If we then map this transcript against the genome, we get the following PAF alignment.

$ minimap2 -x splice --cs genome.fasta cds-transcripts.fa | grep 'OPO1_006919'
OPO1_006919-T1	543	13	543	-	scaffold_9	658044	408903	409554	530	530	60	NM:i:0	ms:i:530	AS:i:466	nn:i:0	ts:A:+	tp:A:P	cm:i:167	s1:i:510	s2:i:0	de:f:0	rl:i:0	cs:Z::129~ct57ac:166~ct64ac:235

The --cs flag in minimap2 can be used to parse the coordinates (below) and you can see we are missing the 5' exon.

>>> cs2coords(408903, 13, 543, '-', ':129~ct57ac:166~ct64ac:235')
([(409320, 409554), (409090, 409255), (408904, 409032)],

So if we run this same alignment with gapmm2 we are able to properly align the 5' terminal exon.

$ gapmm2 genome.fa cds-transcripts.fa | grep 'OPO1_006919'
OPO1_006919-T1	543	0	543	-	scaffold_9	658044	408903	409621	543	543	60	tp:A:P	ts:A:+	NM:i:0	cs:Z::129~ct57ac:166~ct64ac:235~ct54ac:13

>>> cs2coords(408903, 0, 543, '-', ':129~ct57ac:166~ct64ac:235~ct54ac:13')
([(409609, 409621), (409320, 409554), (409090, 409255), (408904, 409032)]

Usage:

gapmm2 can be run as a command line script:

$ gapmm2
usage: gapmm2 [-o] [-t] [-m] [-d] [-h] [--version] reference query

gapmm2: gapped alignment with minimap2. Performs minimap2/mappy alignment with splice options and refines terminal alignments with edlib. Output is PAF format.

Positional arguments:
  reference         reference genome (FASTA)
  query             transcipts in FASTA or FASTQ

Optional arguments:
  -o , --out        output in PAF format (default: stdout)
  -t , --threads    number of threads to use with minimap2 (default: 3)
  -m , --min-mapq   minimum map quality value (default: 1)
  -d, --debug       write some debug info to stderr (default: False)

Help:
  -h, --help        Show this help message and exit
  --version         Show program's version number and exit

It can also be run as a python module. The splice_aligner function will return a list of lists containing PAF formatted data for each alignment and a dictionary of simple stats.

>>> from gapmm2.align import splice_aligner
>>> results, stats = splice_aligner('genome.fa', 'transcripts.fa')
>>> stats
{'n': 6926, 'low-mapq': 0, 'refine-left': 409, 'refine-right': 63}
>>> len(results)
6926
>>> results[0]
['OPO1_000001-T1', 2184, 0, 2184, '+', 'scaffold_1', 1803704, 887, 3127, 2184, 2184, 60, 'tp:A:P', 'ts:A:+', 'NM:i:0', 'cs:Z::958~gt56ag:1226']
>>>

To install the python package, you can do this with pip:

python -m pip install gapmm2

To install the most updated code in master you can run:

python -m pip install git+https://github.com/nextgenusfs/gapmm2.git
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