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

A single molecule sequence assembler for genomes large and small.

hybrid assembly pipeline for bacterial genomes

Text Extraction, Rendering and Converting of PDF Documents

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

quality filtering tool for long reads

adapter trimmer for Oxford Nanopore reads

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Bayesian haplotype-based mutation calling

R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Kraken taxonomic sequence classification system

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which…

Fast HLA type inference from whole-genome data

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

C++ Library to parse Illumina InterOp files

Efficient discovery of overlapping communities in massive networks PK Gopalan, DM Blei Proceedings of the National Academy of Sciences 110 (36), 14534-14539

CutePeaks is a standalone Sanger trace viewer steered by a modern and user-friendly UI.

Useful FILe and stream Operations

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.