LSC is a long read error correction tool developed by Kin Fai Au and Pegah T Afshar. It offers fast correction with high sensitivity and good accuracy.
$ docker run -v $(pwd)/output:/Source/LSC/example/output \
-v $(pwd)/temp:/Source/LSC/example/temp \
-w /Source/LSC/example \
vacation/lsc runLSC.py --long_reads LR.fa \
--short_reads SR.fa --specific_tempdir temp --output outputConstruct prepare volumes that point to your inputs if everything is staged in your working directory it could be run as:
$ docker run -v $(pwd):/home vacation/lsc runLSC.py --long_reads LR.fa \
--short_reads SR.fa --specific_tempdir temp --output outputThe use of --specific_tempdir is pretty import because this folder gets large and it will fill the docker if you don't have it mounted.