slw287r

gtc

Re-implementation of get_trinuc_norm.R of SigMA

Conifer

Calculate confidence scores from Kraken2 output

hg19problematic

Problematic Regions for NGS or Sanger sequencing or very variable regions

Platypus

Platypus Variant Caller

SJM

tapsnp

SNP calling of tet-assisted pyridine borane sequencing (TAPS) data

yapsa

Modified with GRCh38 support

ACEseqWorkflow

Allele-specific copy number estimation with whole genome sequencing

almosthere

Progress indicator library written in C.

cgpBigWig

BigWig manpulation tools using libBigWig and htslib

Complete-Striped-Smith-Waterman-Library

conta

Conta is an R package to detect cross contamination and source of contamination

duf

Disk Usage/Free Utility - a better 'df' alternative

gssw

efficient alignment of strings to partially ordered string graphs

HFU

Beamer theme for the Hochschule Furtwangen University

igv

Local-only version

indelsClassification

R function for the classification of small insertions and deletions for mutational signature analysis.

kmer-cnt

Code examples of fast and simple k-mer counters for tutorial purposes

LaTeX-Graph-Paper

Make your own quadrille, graph, hex, etc paper! Uses the pgf/TikZ package for LaTeX, which should be part of any modern TeX installation.

patchelf

A small utility to modify the dynamic linker and RPATH of ELF executables

QDNAseq.hg38

QDNAseq bin annotation for hg38

sample

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

shallowHRD

This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).

SigMA

Mutational signature analysis for low statistics SNV data

signature.tools.lib

R package containing useful functions for mutational signature analysis

slw287r

TMB_plotter

Python function for TMB snake plots

urmap

URMAP ultra-fast read mapper

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

WFA

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment