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MarBL's Projects

atlas icon atlas

outlier detection in BLAST hits

binnacle icon binnacle

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

canu icon canu

A single molecule sequence assembler for genomes large and small.

chm13 icon chm13

The complete sequence of a human genome

hg002 icon hg002

A complete diploid human genome

hg002-issues icon hg002-issues

HG002 human reference genome issue tracking and polishing

krona icon krona

Interactively explore metagenomes and more from a web browser.

m3 icon m3

Associated materials for the Mid-Atlantic Microbiome Meet-up (M3)

mash icon mash

Fast genome and metagenome distance estimation using MinHash

mashmap icon mashmap

A fast approximate aligner for long DNA sequences

meryl icon meryl

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

meryl-utility icon meryl-utility

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

metacompass icon metacompass

MetaCompass: Reference-guided Assembly of Metagenomes

metamos icon metamos

A metagenomic and isolate assembly and analysis pipeline built with AMOS

mhap icon mhap

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

parsnp icon 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.

primates icon primates

Complete assemblies of non-human primate genomes

rukki icon rukki

Extracting paths from assembly graphs

salsa icon salsa

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

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