PBMM2 ALIGN
Align reads using pbmm2, a minimap2 SMRT wrapper for PacBio data https://github.com/PacificBiosciences/pbmm2/
Example
This wrapper can be used in the following way:
rule pbmm2_align:
input:
reference="target/{reference}.fasta", # can be either genome index or genome fasta
query="{query}.bam", # can be either unaligned bam, fastq, or fasta
output:
bam="aligned/{query}.{reference}.bam",
index="aligned/{query}.{reference}.bam.bai",
log:
"logs/pbmm2_align/{query}.{reference}.log",
params:
preset="CCS", # SUBREAD, CCS, HIFI, ISOSEQ, UNROLLED
sample="", # sample name for @RG header
extra="--sort", # optional additional args
loglevel="INFO",
threads: 12
wrapper:
"v5.0.1/bio/pbmm2/align"
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.
Software dependencies
pbmm2=1.16.0
Code
__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "wrowell@pacb.com"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
tmp_root = snakemake.params.get("tmp_root", None)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
with tempfile.TemporaryDirectory(dir=tmp_root) as tmp_dir:
shell(
"""
(TMPDIR={tmp_dir}; \
pbmm2 align --num-threads {snakemake.threads} \
--preset {snakemake.params.preset} \
--sample {snakemake.params.sample} \
--log-level {snakemake.params.loglevel} \
{extra} \
{snakemake.input.reference} \
{snakemake.input.query} \
{snakemake.output.bam}) {log}
"""
)