marbl/harvest

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Created over 10 years ago
Updated over 3 years ago

marbl/harvest

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CHM13

The complete sequence of a human genome

canu

A single molecule sequence assembler for genomes large and small.

Krona

Interactively explore metagenomes and more from a web browser.

Mash

Fast genome and metagenome distance estimation using MinHash

verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

MashMap

A fast approximate aligner for long DNA sequences

merqury

k-mer based assembly evaluation

Winnowmap

Long read / genome alignment software

SALSA

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

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.

ModDotPlot

MHAP

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

HG002

A complete diploid human genome

metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS

meryl

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

MetaCompass

MetaCompass: Reference-guided Assembly of Metagenomes

Primates

Complete assemblies of non-human primate genomes

MetagenomeScope

Visualization tool for (meta)genome assembly graphs

seqrequester

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

rukki

Extracting paths from assembly graphs

CHM13-issues

CHM13 human reference genome issue tracking

T2T-Browser

Genome browser hub for the T2T genomes and resources

VALET

A pipeline for detecting mis-assemblies in metagenomic assemblies.

gingr

MetaCarvel

MetaCarvel: A scaffolder for metagenomes

MUMmer3

binnacle

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

HG002-issues

HG002 human reference genome issue tracking and polishing

harvest-tools

ATLAS

outlier detection in BLAST hits