lh3 Goto Github PK

alktk

Failed experiment. Archived for a historical record.

asub

A unified array job submitter for LSF, SGE/UGE and Slurm

bcf2

Experimental bcftools port to support BCF2; DEPRECATED by htslib and htsbox

bedtk

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

bfc

High-performance error correction for Illumina resequencing data

bgt

Flexible genotype query among 30,000+ samples whole-genome

bhtsne

Barnes-Hut t-SNE

bioawk

BWK awk modified for biological data

bioconda-recipes

Conda recipes for the bioconda channel.

biofast

Benchmarking programming languages/implementations for common tasks in Bioinformatics

bioseq-js

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

bmif-201

bwa

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

bwa-docker

Minimal docker image for bwa. Not developed any more.

caln50

Compute N50/NG50 and auN/auNG

centos5-vm

Instructions on how to deploy CentOS 5 virtual machines

cgranges

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

chm-eval

chromap

Fast alignment and preprocessing of chromatin profiles

crlf

Concise Run-Length Format for small alphabets; DEPRECATED

dipasm

dipcall

Reference-based variant calling pipeline for a pair of phased haplotype assemblies

dna-nn

Model and predict short DNA sequence features with neural networks

editdist-u85

Fast implementation of Ukkenon's O(ND) algorithm for computing edit distance

etrf

Exact Tandem Repeat Finder (not a TRF replacement)

fastarg

Fast heuristic ARG construction

fermi

A WGS de novo assembler based on the FMD-index for large genomes

fermi-lite

Standalone C library for assembling Illumina short reads in small regions

fermi-paper

The first fermi paper (Li, 2012)

fermi2