Jared Simpson

nanopolish. Signal-level algorithms for MinION data

sga. de novo sequence assembler using string graphs

ncov-tools. Small collection of tools for performing quality control on coronavirus sequencing data and genomes

methylation-analysis. R

nanocorrect. Experimental pipeline for correcting nanopore reads

assembly_accuracy. tools for assessing the accuracy of genome assemblies

nanopore-paper-analysis. Code for nanopore paper

smrest. Tumour-only somatic mutation calling using long reads

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

bam2fastq. Simple convertor from bam to FASTQ

dbgfm. FM-index representation of a de Bruijn graph

nanopore-rna-analysis. Python

mbtools. Rust

ncov-watch. Tools for detecting mutations of interest in SARS-CoV-2 sequencing results

ncov2019-artic-nf. A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

DALIGNER. Find all significant local alignments between reads

gfademo. Small demonstration of the GFA format

sga-extra. Extra tools and utilities for sga

csc2417. Course webpage for CSC2417

tpdb. Python

nanopore_cfdna. Groovy

ncov-random-scripts. Python

bwt-benchmark. Framework to benchmark BWT construction algorithms

modbam_example.

misc. Miscellaenous source code

minimap2. A versatile pairwise aligner for genomic and spliced nucleotide sequences

abyss. de novo sequence assembler

hotaru-analysis. Python