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MarBL (marbl)

MarBL

marbl

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Maryland Bioinformatics Labs

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MarBL's repositories

canu

A single molecule sequence assembler for genomes large and small.

Language:C++Stargazers:649Issues:0Issues:0

HG002

A complete diploid human genome

Stargazers:83Issues:0Issues:0

HG002-issues

HG002 human reference genome issue tracking and polishing

Stargazers:10Issues:0Issues:0

verkko

Language:PythonStargazers:272Issues:0Issues:0

meryl-utility

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

Language:CStargazers:1Issues:0Issues:0

T2T-Browser

Genome browser hub for the T2T genomes and resources

Language:HTMLStargazers:9Issues:0Issues:0

CHM13

The complete sequence of a human genome

License:NOASSERTIONStargazers:887Issues:0Issues:0

merqury

k-mer based assembly evaluation

Language:ShellLicense:NOASSERTIONStargazers:272Issues:0Issues:0

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:0Issues:0

seqrequester

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

Language:CStargazers:23Issues:0Issues:0

ModDotPlot

Language:PythonLicense:MITStargazers:101Issues:0Issues:0

Winnowmap

Long read / genome alignment software

Language:CLicense:NOASSERTIONStargazers:233Issues:0Issues:0

training

Genome Assembly 102

Language:ShellStargazers:6Issues:0Issues:0

SALSA

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

Language:PythonLicense:MITStargazers:172Issues:0Issues:0

meryl

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

Language:CStargazers:111Issues:0Issues:0

Primates

Complete assemblies of non-human primate genomes

License:NOASSERTIONStargazers:32Issues:0Issues:0

rukki

Extracting paths from assembly graphs

Language:RustStargazers:19Issues:0Issues:0

canu-regression

Regression test cases and results for Canu.

Language:ShellStargazers:0Issues:0Issues:0

MashMap

A fast approximate aligner for long DNA sequences

Language:C++License:NOASSERTIONStargazers:259Issues:0Issues:0

verkko-regression

Test suite for Verkko.

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CHM13-issues

CHM13 human reference genome issue tracking

Language:HTMLLicense:NOASSERTIONStargazers:18Issues:0Issues:0

MetagenomeScope

Visualization tool for (meta)genome assembly graphs

Language:JavaScriptLicense:GPL-3.0Stargazers:24Issues:0Issues:0

harvest-tools

Language:C++License:NOASSERTIONStargazers:8Issues:0Issues:0

gingr

Language:C++License:NOASSERTIONStargazers:13Issues:0Issues:0

Mash

Fast genome and metagenome distance estimation using MinHash

Language:C++License:NOASSERTIONStargazers:381Issues:0Issues:0

MHAP

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

Language:JavaLicense:Apache-2.0Stargazers:95Issues:0Issues:0

MUMmer3

MUMmer3

Language:C++License:NOASSERTIONStargazers:15Issues:0Issues:0

Krona

Interactively explore metagenomes and more from a web browser.

Language:JavaScriptStargazers:459Issues:0Issues:0

binnacle

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

Language:PythonStargazers:10Issues:0Issues:0

MetaCarvel

MetaCarvel: A scaffolder for metagenomes

Language:C++License:MITStargazers:13Issues:0Issues:0