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abyss

de novo sequence assembler

align

Sequence Alignment and Scoring

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

artic-tools

a set of tools for viral amplicon schemes

assembly_accuracy

tools for assessing the accuracy of genome assemblies

bam2fastq

Simple convertor from bam to FASTQ

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

beetl

BEETL

bioconda-recipes

Conda recipes for the bioconda channel.

bri

Bam Read Index - Extract alignments from a bam file by readname

bwt-benchmark

Framework to benchmark BWT construction algorithms

canu

A single molecule sequence assembler for genomes large and small.

cbw-idge-2023

csc2417

Course webpage for CSC2417

daligner

Find all significant local alignments between reads

dbgfm

FM-index representation of a de Bruijn graph

dwgsim

Whole Genome Simulator for Next-Generation Sequencing

fast5

fieldbioinformatics

The ARTIC field bioinformatics pipeline

flappie

Flip-flop basecaller for Oxford Nanopore reads

gfademo

Small demonstration of the GFA format

homebrew-science

Scientific formulae for the Homebrew package manager

hts-specs

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

hts-sys

Raw rust bindings for htslib

htslib

C library for high-throughput sequencing data formats

ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

khmer

in-memory k-mer counting

longshot

diploid SNV caller for error-prone reads

mbtools

methylation-analysis