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.
How to run from Docker
Running the included example data:
$ 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 output
Running the command on your data:
Construct 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 output
The 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.