MINIMAP2¶
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
URL: https://lh3.github.io/minimap2
Example¶
This wrapper can be used in the following way:
rule minimap2_paf:
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
sorting="coordinate", # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
sort_extra="", # optional: extra arguments for samtools/picard
threads: 3
wrapper:
"v1.16.0/bio/minimap2/aligner"
rule minimap2_sam:
input:
target="target/{input1}.mmi", # can be either genome index or genome fasta
query=["query/reads1.fasta", "query/reads2.fasta"],
output:
"aligned/{input1}_aln.sam",
log:
"logs/minimap2/{input1}.log",
params:
extra="-x map-pb", # optional
sorting="none", # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
sort_extra="", # optional: extra arguments for samtools/picard
threads: 3
wrapper:
"v1.16.0/bio/minimap2/aligner"
rule minimap2_sam_sorted:
input:
target="target/{input1}.mmi", # can be either genome index or genome fasta
query=["query/reads1.fasta", "query/reads2.fasta"],
output:
"aligned/{input1}_aln.sorted.sam",
log:
"logs/minimap2/{input1}.log",
params:
extra="-x map-pb", # optional
sorting="queryname", # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
sort_extra="", # optional: extra arguments for samtools/picard
threads: 3
wrapper:
"v1.16.0/bio/minimap2/aligner"
rule minimap2_bam_sorted:
input:
target="target/{input1}.mmi", # can be either genome index or genome fasta
query=["query/reads1.fasta", "query/reads2.fasta"],
output:
"aligned/{input1}_aln.sorted.bam",
log:
"logs/minimap2/{input1}.log",
params:
extra="-x map-pb", # optional
sorting="coordinate", # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
sort_extra="", # optional: extra arguments for samtools/picard
threads: 3
wrapper:
"v1.16.0/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.
Notes¶
- The extra param allows for additional arguments for minimap2.
- The sort param allows to enable sorting (if output not PAF), and can be either ‘none’, ‘queryname’ or ‘coordinate’.
- The sort_extra allows for extra arguments for samtools/picard
Software dependencies¶
minimap2=2.24
samtools
snakemake-wrapper-utils=0.4
Authors¶
- Tom Poorten
- Michael Hall
- Filipe G. Vieira
Code¶
__author__ = "Tom Poorten"
__copyright__ = "Copyright 2017, Tom Poorten"
__email__ = "tom.poorten@gmail.com"
__license__ = "MIT"
from os import path
from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import infer_out_format
from snakemake_wrapper_utils.samtools import get_samtools_opts
samtools_opts = get_samtools_opts(snakemake, parse_output=False)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
sort = snakemake.params.get("sorting", "none")
sort_extra = snakemake.params.get("sort_extra", "")
out_ext = infer_out_format(snakemake.output[0])
pipe_cmd = ""
if out_ext != "PAF":
# Add option for SAM output
extra += " -a"
# Determine which pipe command to use for converting to bam or sorting.
if sort == "none":
if out_ext != "SAM":
# Simply convert to output format using samtools view.
pipe_cmd = f"| samtools view -h {samtools_opts}"
elif sort in ["coordinate", "queryname"]:
# Add name flag if needed.
if sort == "queryname":
sort_extra += " -n"
# Sort alignments.
pipe_cmd = f"| samtools sort {sort_extra} {samtools_opts}"
else:
raise ValueError(f"Unexpected value for params.sort: {sort}")
shell(
"(minimap2"
" -t {snakemake.threads}"
" {extra} "
" {snakemake.input.target}"
" {snakemake.input.query}"
" {pipe_cmd}"
" > {snakemake.output[0]}"
") {log}"
)