MINIMAP2¶
A versatile pairwise aligner for genomic and spliced nucleotide sequences https://lh3.github.io/minimap2
Software dependencies¶
- minimap2 ==2.5
Example¶
This wrapper can be used in the following way:
rule minimap2:
input:
target="target/{input1}.mmi", # can be either genome index or genome fasta
query=["query/reads1.fasta", "query/reads2.fasta"]
output:
"aligned/{input1}_aln.paf"
log:
"logs/minimap2/{input1}.log"
params:
extra="-x map-pb" # optional
threads: 3
wrapper:
"0.26.1/bio/minimap2/aligner"
Note that input, output and log file paths can be chosen freely. When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Authors¶
- Tom Poorten
Code¶
__author__ = "Tom Poorten"
__copyright__ = "Copyright 2017, Tom Poorten"
__email__ = "tom.poorten@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
inputQuery = " ".join(snakemake.input.query)
shell("(minimap2 -t {snakemake.threads} {extra} "
"{snakemake.input.target} {inputQuery} >"
"{snakemake.output[0]}) {log}")