Giters
MarBL (marbl)

MarBL

marbl

Geek Repo

Maryland Bioinformatics Labs

Github PK Tool:Github PK Tool

MarBL's repositories

CHM13

The complete sequence of a human genome

License:NOASSERTIONStargazers:887Issues:66Issues:93

canu

A single molecule sequence assembler for genomes large and small.

Language:C++Stargazers:649Issues:54Issues:2278

Krona

Interactively explore metagenomes and more from a web browser.

Language:JavaScriptStargazers:459Issues:39Issues:176

Mash

Fast genome and metagenome distance estimation using MinHash

Language:C++License:NOASSERTIONStargazers:381Issues:33Issues:165

merqury

k-mer based assembly evaluation

Language:ShellLicense:NOASSERTIONStargazers:272Issues:12Issues:127

verkko

Language:PythonStargazers:272Issues:17Issues:256

MashMap

A fast approximate aligner for long DNA sequences

Language:C++License:NOASSERTIONStargazers:259Issues:17Issues:47

Winnowmap

Long read / genome alignment software

Language:CLicense:NOASSERTIONStargazers:233Issues:15Issues:45

SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data

Language:PythonLicense:MITStargazers:172Issues:21Issues:165

parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

Language:C++License:NOASSERTIONStargazers:123Issues:12Issues:127

meryl

A genomic k-mer counter (and sequence utility) with nice features.

Language:CStargazers:111Issues:11Issues:45

ModDotPlot

Language:PythonLicense:MITStargazers:101Issues:11Issues:16

MHAP

MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities

Language:JavaLicense:Apache-2.0Stargazers:95Issues:16Issues:18

HG002

A complete diploid human genome

Stargazers:83Issues:12Issues:6

Primates

Complete assemblies of non-human primate genomes

License:NOASSERTIONStargazers:32Issues:9Issues:1

MetagenomeScope

Visualization tool for (meta)genome assembly graphs

Language:JavaScriptLicense:GPL-3.0Stargazers:24Issues:9Issues:223

seqrequester

A tool for summarizing, extracting, generating and modifying DNA sequences.

Language:CStargazers:23Issues:7Issues:8

rukki

Extracting paths from assembly graphs

Language:RustStargazers:19Issues:6Issues:29

CHM13-issues

CHM13 human reference genome issue tracking

Language:HTMLLicense:NOASSERTIONStargazers:18Issues:9Issues:6

MUMmer3

MUMmer3

Language:C++License:NOASSERTIONStargazers:15Issues:8Issues:9

gingr

Language:C++License:NOASSERTIONStargazers:13Issues:12Issues:19

MetaCarvel

MetaCarvel: A scaffolder for metagenomes

Language:C++License:MITStargazers:13Issues:11Issues:11

binnacle

Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins

Language:PythonStargazers:10Issues:8Issues:3

HG002-issues

HG002 human reference genome issue tracking and polishing

Stargazers:10Issues:17Issues:684

harvest-tools

Language:C++License:NOASSERTIONStargazers:8Issues:12Issues:21

T2T-Browser

Genome browser hub for the T2T genomes and resources

Language:HTMLStargazers:8Issues:8Issues:0

training

Genome Assembly 102

Language:ShellStargazers:6Issues:6Issues:0

meryl-utility

A collection of miscellaneous code used by Meryl, Canu and others.

Language:CStargazers:1Issues:7Issues:1

canu-regression

Regression test cases and results for Canu.

Language:ShellStargazers:0Issues:3Issues:0

verkko-regression

Test suite for Verkko.

Language:PerlStargazers:0Issues:6Issues:0