37 open source projects by lh3

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Proof-of-concept seq-to-graph mapper and graph generator

Reads simulator

Fast multi-line FASTA/Q reader in several programming languages

Code examples of fast and simple k-mer counters for tutorial purposes

Benchmarking programming languages/implementations for common tasks in Bioinformatics

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

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

This repo is DEPRECATED. Please use minimap2, the successor of minimap.

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

Model and predict short DNA sequence features with neural networks

Toolkit for processing TAB-delimited format

Exact Tandem Repeat Finder (not a TRF replacement)

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Toolkit for processing sequences in FASTA/Q formats

BWK awk modified for biological data

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

De novo assembly based variant calling pipeline for Illumina short reads

Useful small programs

This is *NOT* the official repository of samtools.

No description, website, or topics provided.

Compute N50/NG50 and auN/auNG

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

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

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang

FermiKit small variant calls for public SGDP samples

Incremental construction of FM-index for DNA sequences

Tools to process LIANTI sequence data

Wrapper for RTG's vcfeval; DEPRECATED!

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Symmetric DUST for finding low-complexity regions in DNA sequences

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

High-performance error correction for Illumina resequencing data

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