Eigen tools by Nick Patterson and Alkes Price lab

UCSC command line bioinformatic utilities

Simple oligo analysis and primer design

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

LongQC is a tool for the data quality control of the PacBio and ONT long reads.

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs a…

Yet another Hi-C scaffolding tool

Nanopore data assembler

Microassembly based somatic variant caller for NGS data

Match up paired end fastq files quickly and efficiently.

Yet another k-mer analyzer

A genomic k-mer counter (and sequence utility) with nice features.

Global alignment and alignment extension

Haplotype based scans for selection

Ultra-fast de novo assembler using long noisy reads

Tools to work with GWAS-VCF summary statistics files

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group

A local-haplotagging-based small and structural variant caller

EasyCodeML: A visual tool for analysis of selection using CodeML

PHAST

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds

Adaptive semi-global banded alignment on string graphs

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Exact Tandem Repeat Finder (not a TRF replacement)

Sequence analysis library used by Eddy/Rivas lab code