Bowtie2
Bowtie2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. here
Available containers
| Name | sha256 | mpi | labels | descripion |
|---|---|---|---|---|
| Singularity.Bowtie2-2.4.4-GCC-10.3.0.localimage.sif | 6ab2b3a61866d24d1afbe81291f769c418b93547d3377ecba63935ad1a807050 | none | none | benchmark |
Running the container
Example invocation of Bowtie2 benchmark
# Note: $PLCR is base path of container repository and $CONT is the container filename
cd $TMPDIR
wget '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 bowtie2-build 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 bowtie2 --very-sensitive -x hg38 -1 ERR2356727_1.fastq -2 ERR2356727_2.fastq -S ERR.sam -p 4 #$SLURM_NTASKS