Hidden State Speciation and Extinction

Share, discover, and collect prompts from the community. Free and open source — self-host for your organization with complete privacy.

The second version of the Kraken taxonomic sequence classification system

Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis

Tools for data handling and analysis in macroecology

An R package for the calculation of taxonomic, phenotypic and phylogenetic metrics across grid cells.

Phylogenetic orthology inference for comparative genomics

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

C++ API & command-line toolkit for working with BAM data

Simulators of spatial genetic diversity: for non-programmers and researchers!

Software to construct and analyse KewTreeOfLife (PAFTOL project)

mapping pipeline for ancient DNA

A structural variation pipeline for short-read sequencing

A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

deep learning prediction of geographic location from individual genome sequences

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

Tools to work with variant call format files

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Pipelines and tools for the processing of ancient and modern HTS data.

The next version of bwa-mem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

k-mer based assembly evaluation

Transcript assembly and quantification for RNA-Seq

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Aggregate results from bioinformatics analyses across many samples into a single report.

This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster

R Port of psmc

iTerm2 is a terminal emulator for Mac OS X that does amazing things.