SAMtools
SAMtools is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. More information can be found here
Available containers
| Name | sha256 | mpi | labels | descripion |
|---|---|---|---|---|
| Singularity.SAMtools-1.13-GCC-10.3.0.localimage.sif | 5a363de7d5778ffb08d1cf65941e2f863a42dd2e0d3f3e313d028a787387f01a | none | none | benchmark |
Running the container
Example invocation of SAMtools benchmark
# Note: $PLCR is base path of container repository and $CONT is the container filename
cd $TMPDIR
wget -q 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshS3AlnRep1.bam'
mv wgEncodeUwRepliSeqSknshS3AlnRep1.bam eg.bam
time singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT samtools sort -n eg.bam -o egs.bam