Parascopy: Tool for robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing (short reads)

Longshot: Variant calling tool for diploid genomes using long error prone read sequencing such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore (ONT)

HapCUT2: new version of HapCUT that uses a likelihood based model for haplotype assembly and can model trans-errors in Hi-C data. A related method for integrated read-based and population-based phasing is also available on github

CRISP: program for detection of SNVs and short insertion/deletion variants from high-throughput sequencing of pooled DNA samples. Latest source code is available from github

iAdmix a program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping). Source code is available from github

Software that is no longer updated:

PCRduplicates Computational method to estimate the PCR duplication rate in high-throughput DNA sequencing experiments

Hap-simulator a program for simulating reads for haplotype assembly to evaluate N50 metrics as a function of read length, insert size (paired-end reads), etc

HapCUT: a program for haplotype assembly or haplotype phasing using sequence reads from a diploid genome. Source code is available from github

piCALL a probabilistic method for detection of insertion/deletion polymorphisms (indels) from population-scale sequence data (use CRISP instead of piCALL)

SNIP-Seq one of the first methods designed to leverage sequence data from multiple individuals simultaneously to model site-specific error rates and detect SNPs

HASH implementation of an MCMC algorithm for haplotype assembly from whole-genome sequence data (use HapCUT instead)

LUBOUND program to calculate lower bounds on the minimum number of recombination events in a sample history