pvdam3

Peter van Dam's starred repositories

biopython

Official git repository for Biopython (originally converted from CVS)

Language:PythonNOASSERTION4258 168 1675

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

Language:PythonGPL-3.0773 34 513

OrthoFinder

Phylogenetic orthology inference for comparative genomics

Language:PythonGPL-3.0653 27 887

biocode

Bioinformatics code libraries and scripts

Language:PythonMIT478 31 59

jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

Language:JavaScriptNOASSERTION460 52 1256

velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829

Language:CGPL-2.0278 29 37

MashMap

A fast approximate aligner for long DNA sequences

Language:C++NOASSERTION260 17 47

smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Language:RApache-2.0223 10 145

sickle

Windowed Adaptive Trimming for fastq files using quality

Language:CMIT220 21 33

nanopack

An overview of all nanopack tools

Language:PythonGPL-3.0200 9 12

fastx_toolkit

FASTA/FASTQ pre-processing programs

Language:CNOASSERTION160 18 22

alfred

BAM Statistics, Feature Counting and Annotation

Language:C++BSD-3-Clause136 9 44

assembly-stats

Get assembly statistics from FASTA and FASTQ files

Language:C++NOASSERTION110 18 5

MITObim

MITObim - mitochondrial baiting and iterative mapping

Language:PerlMIT107 11 53

TMAP

Torrent Mapping Alignment Program

Language:CGPL-2.049 23 14

blobology

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)

Language:PerlMIT46 15 8

scripts

Metagenomic pipeline and other general scripts used in the lab.

Language:PerlGPL-3.034 9 3

grabb

GRAbB (Genome Region Assembly by Baiting) is a program designed to assemble selected regions of the genome or transcriptome using reference sequences and NGS data.

Language:CMIT11 4 3

Raspberry

Raspberry Pi projects

Language:PHPBSD-2-Clause400