MarBL (@marbl)
  • Stars
    star
    3,682
  • Global Org. Rank 5,928 (Top 2 %)
  • Registered almost 11 years ago
  • Most used languages
    C++
    30.8 %
    Python
    23.1 %
    C
    11.5 %
    JavaScript
    7.7 %
    HTML
    7.7 %
    TeX
    3.8 %
    Rust
    3.8 %
    Roff
    3.8 %
    Java
    3.8 %
    Shell
    3.8 %

Top repositories

1

CHM13

The complete sequence of a human genome
914
star
2

canu

A single molecule sequence assembler for genomes large and small.
C++
600
star
3

Krona

Interactively explore metagenomes and more from a web browser.
JavaScript
419
star
4

Mash

Fast genome and metagenome distance estimation using MinHash
C++
355
star
5

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.
Python
274
star
6

MashMap

A fast approximate aligner for long DNA sequences
C++
210
star
7

merqury

k-mer based assembly evaluation
Shell
201
star
8

Winnowmap

Long read / genome alignment software
C
187
star
9

SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data
Python
178
star
10

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.
C++
124
star
11

ModDotPlot

Python
102
star
12

MHAP

MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities
Java
95
star
13

HG002

A complete diploid human genome
94
star
14

metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
Roff
93
star
15

meryl

A genomic k-mer counter (and sequence utility) with nice features.
C
78
star
16

harvest

50
star
17

MetaCompass

MetaCompass: Reference-guided Assembly of Metagenomes
Python
38
star
18

Primates

Complete assemblies of non-human primate genomes
38
star
19

MetagenomeScope

Visualization tool for (meta)genome assembly graphs
JavaScript
25
star
20

seqrequester

A tool for summarizing, extracting, generating and modifying DNA sequences.
C
23
star
21

rukki

Extracting paths from assembly graphs
Rust
22
star
22

CHM13-issues

CHM13 human reference genome issue tracking
HTML
18
star
23

T2T-Browser

Genome browser hub for the T2T genomes and resources
HTML
15
star
24

VALET

A pipeline for detecting mis-assemblies in metagenomic assemblies.
TeX
14
star
25

gingr

C++
13
star
26

MetaCarvel

MetaCarvel: A scaffolder for metagenomes
C++
13
star
27

MUMmer3

MUMmer3
C++
11
star
28

binnacle

Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins
Python
10
star
29

HG002-issues

HG002 human reference genome issue tracking and polishing
10
star
30

harvest-tools

C++
8
star
31

ATLAS

outlier detection in BLAST hits
Python
3
star