Pinned Repositories
canu
A single molecule sequence assembler for genomes large and small.
CHM13
The complete sequence of a human genome
Krona
Interactively explore metagenomes and more from a web browser.
Mash
Fast genome and metagenome distance estimation using MinHash
MashMap
A fast approximate aligner for long DNA sequences
merqury
k-mer based assembly evaluation
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.
SALSA
SALSA: A tool to scaffold long read assemblies with Hi-C data
verkko
Winnowmap
Long read / genome alignment software
MarBL's Repositories
marbl/CHM13
The complete sequence of a human genome
marbl/canu
A single molecule sequence assembler for genomes large and small.
marbl/Krona
Interactively explore metagenomes and more from a web browser.
marbl/Mash
Fast genome and metagenome distance estimation using MinHash
marbl/merqury
k-mer based assembly evaluation
marbl/verkko
marbl/MashMap
A fast approximate aligner for long DNA sequences
marbl/Winnowmap
Long read / genome alignment software
marbl/SALSA
SALSA: A tool to scaffold long read assemblies with Hi-C data
marbl/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.
marbl/meryl
A genomic k-mer counter (and sequence utility) with nice features.
marbl/ModDotPlot
marbl/MHAP
MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities
marbl/HG002
A complete diploid human genome
marbl/Primates
Complete assemblies of non-human primate genomes
marbl/MetagenomeScope
Visualization tool for (meta)genome assembly graphs
marbl/seqrequester
A tool for summarizing, extracting, generating and modifying DNA sequences.
marbl/rukki
Extracting paths from assembly graphs
marbl/CHM13-issues
CHM13 human reference genome issue tracking
marbl/MUMmer3
MUMmer3
marbl/gingr
marbl/MetaCarvel
MetaCarvel: A scaffolder for metagenomes
marbl/binnacle
Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins
marbl/HG002-issues
HG002 human reference genome issue tracking and polishing
marbl/harvest-tools
marbl/T2T-Browser
Genome browser hub for the T2T genomes and resources
marbl/training
Genome Assembly 102
marbl/meryl-utility
A collection of miscellaneous code used by Meryl, Canu and others.
marbl/canu-regression
Regression test cases and results for Canu.
marbl/verkko-regression
Test suite for Verkko.