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Humam Siga's Projects

bsseq2 icon bsseq2

Analysing whole genome BS and hBS sequencing data

copycat icon copycat

Copycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)

cue icon cue

Deep learning framework for SV calling and genotyping

grocsvs icon grocsvs

Genome-wide reconstruction of complex structural variants

mutscape icon mutscape

Ａ user-friendly Python toolkit, which provides a comprehensive pipeline to easily explore the cohort-based mutational characterization for studying cancer genomics.

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