Beast code in Giters

Kim Ferguson's starred repositories

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Language:CNOASSERTION1763 86 1110

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Language:CGPL-3.01512 108 304

canu

A single molecule sequence assembler for genomes large and small.

Language:C++653 54 2288

NanoPlot

Plotting scripts for long read sequencing data

Language:PythonMIT412 12 336

pilon

Pilon is an automated genome assembly improvement and variant detection tool

Language:ScalaGPL-2.0338 30 170

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

Language:C++MIT268 22 234

quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Language:C++GPL-3.0198 12 72

nanofilt

Filtering and trimming of long read sequencing data

Language:PythonGPL-3.0185 10 58

kentUtils

UCSC command line bioinformatic utilities

Language:C166 450

adegenet

adegenet: a R package for the multivariate analysis of genetic markers

Language:R165 26 283

nanostat

Create statistic summary of an Oxford Nanopore read dataset

Language:PythonGPL-3.090 3 35

nanoQC

Quality control tools for nanopore sequencing data

Language:PythonGPL-3.088 9 16

DBG2OLC

A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

Language:C++GPL-3.066 7 67

fmlrc

a long-read error correction tool using the multi-string Burrows Wheeler Transform

Language:C++MIT43 2 20

pegas

Population and Evolutionary Genetics Analysis System

Language:RGPL-2.027 6 80

hierfstat

the hierfstat package

Language:HTML24 9 66

ddRADseqTools

Software package for in silico simulation and testing of double digest RADseq experiments.

Language:PythonGPL-3.018 2 11

multifastats

Multifastats: Multi-Fasta Sequence Stats. Free python-based program that, from a set of a set of 'fasta' sequences (as group or individually), produces basic outputs and statistics (N50, %GC, molecular weight, cut in kmers and concatenate sequences using defined spacers). And also allows to apply some filters and select subgroups by length and/or type. This runs in Windows, Linux and Mac OS.

Language:PythonNOASSERTION12 2 1

kfergy