HAPCUT¶

Description¶

HapCUT is a max-cut based algorithm for haplotype assembly that uses the mix of sequenced fragments from the two chromosomes of an individual, this program can be applied to sequence data generated from next-generation sequencing platforms. HapCUT takes as input the aligned SAM/BAM files for an individual diploid genome and the list of variants, and outputs the phased haplotype blocks that can be assembled from the sequence reads.

Environment Modules¶

Run module spider hapcut to find out what environment modules are available for this application.

Environment Variables¶

HPC_HAPCUT_DIR - installation directory
HPC_HAPCUT_BIN - executable directory
HPC_HAPCUT_EXE - example directory

Categories¶

biology, assembly