Exonerate
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics. More information here
Available containers
| Name | sha256 | mpi | labels | descripion |
|---|---|---|---|---|
| Singularity.Exonerate-2.4.0-foss-2021b.localimage.sif | 0f4a9bb4c577fbf6492bedd96d09432e3a557c29b6a9e5c869527a251b64b81c | none | none | benchmark |
Running the container
Example invocation of Exonerate benchmark
cd $TMPDIR
wget 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz'
gzip -dk hg38.fa.gz
mv $TMPDIR/hg38.fa $TMPDIR/hg38.fasta
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 ERR2356727/ERR2356727.sra
sed -n '1~4s/^@/>/p;2~4p' ERR2356727.fastq > ERR2356727.fasta
time singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT exonerate ERR2356727.fasta hg38.fasta --cores 48