Martin Pollard's repositories
juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
nf-core_configs
working fork of NF cores Config files used to define parameters specific to compute environments at different Institutions
htslib
C library for high-throughput sequencing data formats (MP15 private repo)
bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
samtools
MP15's working samtools repo (not official release expect rebases)
bwa
Burrow-Wheeler Aligner
hapdup
Pipeline to convert a haploid assembly into diploid (working copy)
dorado
Oxford Nanopore's Basecaller (mp15 working copy)
sniffles_circos
A way to make a CIRCOS plot of Sniffles BED files
whatshap
(private dev repo) Read-based phasing of genomic variants, also called haplotype assembly
FastQ-Screen
(working copy) Detecting contamination in NGS data and multi-species analysis
py-cpuinfo
A module for getting CPU info with pure Python (working tree)
minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
codecarbon
mp15's working fork of codecarbon for Pull requests etc.
bwa-mem2
MP15's private working fork of bwa-mem2
graviton-builder
CDK builder for building graviton hosts for the benchmark suite
webatlas-app
(fork for edits only) An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.
tombo
Private fork of Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
genomicsbench
A benchmark suite to study the performance characteristics of genomics applications
WSL2-Linux-Kernel
The source for the Linux kernel used in Windows Subsystem for Linux 2 (WSL2)
VariantWorks
Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/
BioNanoAnalyst
BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.
pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
FALCON
FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
npg_conda
NPG Conda recipes and tools
irods
Open Source Data Management Software
perl-irods-wrap
Perl iRODS Client Wrapper Library
nvbio
NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.
npg_seq_pipeline
Processing and analysis of data coming from Illumina sequencing machines
npg_irods
Tools for managing HTS (BAM and CRAM) format files in iRODS.