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samtools

Martin Pollard's repositories

agp_tools

Set of tools for working with scaffolds and AGP files

Language:CGPL-3.0020

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

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BioNanoAnalyst

BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.

Language:PythonGPL-3.0020

bwa-mem2

MP15's private working fork of bwa-mem2

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codecarbon

mp15's working fork of codecarbon for Pull requests etc.

Language:Jupyter NotebookMIT000

dorado

Oxford Nanopore's Basecaller (mp15 working copy)

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FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

Language:PythonNOASSERTION020

FastQ-Screen

(working copy) Detecting contamination in NGS data and multi-species analysis

GPL-3.0000

genomicsbench

A benchmark suite to study the performance characteristics of genomics applications

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graviton-builder

CDK builder for building graviton hosts for the benchmark suite

Language:Python010

hapdup

Pipeline to convert a haploid assembly into diploid (working copy)

NOASSERTION000

htslib

C library for high-throughput sequencing data formats (MP15 private repo)

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irods

Open Source Data Management Software

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minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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nf-core_configs

working fork of NF cores Config files used to define parameters specific to compute environments at different Institutions

MIT000

npg_conda

NPG Conda recipes and tools

Language:Shell010

npg_irods

Tools for managing HTS (BAM and CRAM) format files in iRODS.

Language:PerlGPL-3.0010

npg_seq_pipeline

Processing and analysis of data coming from Illumina sequencing machines

Language:Perl010

npg_tracking

WTSI Illumina sequencing instruments (HiSeq, MiSeq, GA) tracking

Language:Perl010

nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

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perl-irods-wrap

Perl iRODS Client Wrapper Library

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py-cpuinfo

A module for getting CPU info with pure Python (working tree)

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pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

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samtools

MP15's working samtools repo (not official release expect rebases)

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sniffles_circos

A way to make a CIRCOS plot of Sniffles BED files

Language:RGPL-3.0000

tombo

Private fork of Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

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VariantWorks

Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/

Apache-2.0000

webatlas-app

(fork for edits only) An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.

Language:JavaScriptMIT000

whatshap

(private dev repo) Read-based phasing of genomic variants, also called haplotype assembly

Language:PythonMIT000

WSL2-Linux-Kernel

The source for the Linux kernel used in Windows Subsystem for Linux 2 (WSL2)

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