BWA
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. here
Available containers
| Name | sha256 | mpi | labels | descripion |
|---|---|---|---|---|
| Singularity.BWA-0.7.17-intel-2021b.localimage.sif | fe96b0ffc5287ef62b8fa6c15f3c5831225cf206fdd2e2809edc9834fcccfd92 | none | none | benchmark |
Running the container
Example invocation of BWA benchmark
cd $TMPDIR
wget- q 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz'
gzip -dk hg38.fa.gz
singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT bwa index -a bwtsw hg38.fa hg38
singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT prefetch ERR2356727
singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT fastq-dump --split-files ERR2356727/ERR2356727.sra
time singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT bwa mem -t $SLURM_NTASKS hg38.fa ERR2356727_1.fastq ERR2356727_2.fastq > ERR.sam