Toolkit for processing sequences in FASTA/Q formats

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

📖 An opinionated intermediate/advanced Git book

Python library to handle Gene Ontology (GO) terms

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Automatically exported from code.google.com/p/cdhit

Specifications of SAM/BAM and related high-throughput sequencing file formats

Population genetics notes

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Signal-level algorithms for MinION data

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Transcript assembly and quantification for RNA-Seq

Automatically exported from code.google.com/p/figtree

Genome-wide Efficient Mixed Model Association

lumpy: a general probabilistic framework for structural variant discovery

A comparison of different Oxford Nanopore basecallers

Program for analysing NGS data.

adegenet: a R package for the multivariate analysis of genetic markers

Programs to analyse NGS data for population genetics purposes

Minimalist alternatives to "best practices" paper

Software for painlessly estimating average nucleotide diversity within and between populations

A variational framework for inferring population structure from SNP genotype data.

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery

💻 command-line bootcamp adventure in your browser

A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.

Collection of various scripts

Software for clustering de novo assembled transcripts and counting overlapping reads

An R package of map layers for British Columbia

🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction