Ongoing work
Clustering PacBio reads into their original chromosomes and directionalities using Strand-seq data - summarized in a Snakemake pipeline.
Download the pipeline Download the pipeline directory including Snakefile, the perl script processMinimaptab.pl, and a subdirectory "utils" containing the following Rscripts:
Install required software:
Prepare the input data
Set up the parameters of the snakemake pipeline
Snakefile
and set the parameters of minimap and SaaRclust at the beginning of the file
(such as Mosaicatcher) and to the R scripts.Run Snakemake
snakemake
to compute all tasks locallySnakemake creates the following output files and directories:
Minimap alignment results in directory "aligns"
SaaRclust results
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