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/metAMOS
A metagenomic and isolate assembly and analysis pipeline built with AMOS
marbl/VALET
A pipeline for detecting mis-assemblies in metagenomic assemblies.
marbl/gingr
marbl/M3
Associated materials for the Mid-Atlantic Microbiome Meet-up (M3)
marbl/metaValidate
marbl/seminars
Seminar announcements