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Eric Edsinger (000generic)

000generic

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Location:Campeche, Mexico

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Eric Edsinger's starred repositories

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

Language:CLicense:GPL-3.0Stargazers:1370Issues:32Issues:824

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Language:C++License:GPL-3.0Stargazers:773Issues:38Issues:830

canu

A single molecule sequence assembler for genomes large and small.

Language:C++Stargazers:654Issues:54Issues:2295

Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

Language:C++License:GPL-3.0Stargazers:582Issues:37Issues:109

hh-suite

Remote protein homology detection suite.

Language:CLicense:GPL-3.0Stargazers:529Issues:25Issues:322

interproscan

Genome-scale protein function classification

Language:JavaLicense:Apache-2.0Stargazers:292Issues:18Issues:323

velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829

Language:CLicense:GPL-2.0Stargazers:281Issues:29Issues:37

shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Language:C++License:NOASSERTIONStargazers:271Issues:23Issues:106

masurca

Language:M4License:GPL-3.0Stargazers:243Issues:16Issues:341

kraken

Kraken taxonomic sequence classification system

Language:C++License:GPL-3.0Stargazers:212Issues:27Issues:135

RaGOO

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

Language:PythonLicense:MITStargazers:170Issues:6Issues:80

idba

Language:C++Stargazers:124Issues:11Issues:58

bionitio

Demonstrating best practices for bioinformatics command line tools

Language:ShellLicense:MITStargazers:116Issues:7Issues:51

transrate

Understand your transcriptome assembly

Language:RubyLicense:NOASSERTIONStargazers:100Issues:12Issues:179

dammit

just annotate it, dammit!

Language:PythonLicense:NOASSERTIONStargazers:88Issues:13Issues:165

Rcorrector

Error correction for Illumina RNA-seq reads

Language:C++License:GPL-3.0Stargazers:63Issues:7Issues:37

oases

De novo transcriptome assembler for short reads

Language:CLicense:GPL-3.0Stargazers:62Issues:9Issues:21

crb-blast

Conditional Reciprocal Best Blast

Language:RubyStargazers:40Issues:6Issues:10

transfuse

Merge transcriptome assemblies

Language:RubyStargazers:29Issues:8Issues:17

snapr

SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis

Language:C++License:Apache-2.0Stargazers:25Issues:10Issues:6

shmlast

blast, shmlast

Language:PythonLicense:NOASSERTIONStargazers:21Issues:3Issues:7

Rascaf

Scaffolding with RNA-seq read alignment

Language:CStargazers:20Issues:5Issues:23

AGOUTI

Annotated Genome Optimization Using Transcriptome Information

Language:PythonLicense:MITStargazers:20Issues:3Issues:18

P_RNA_scaffolder

use paired-end transcriptome reads to scaffold genomes

Language:PerlStargazers:10Issues:0Issues:6

TBro

Visualization and management of denovo transcriptomes

Language:PHPStargazers:10Issues:6Issues:58

HaMStR

Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.

Language:PerlLicense:GPL-3.0Stargazers:9Issues:9Issues:20

csblast

Context-specific mutation probabilities for protein sequencing searching.

Language:C++License:NOASSERTIONStargazers:5Issues:6Issues:0

csblast

Context-specific mutation probabilities for protein sequencing searching.

Language:C++License:NOASSERTIONStargazers:3Issues:2Issues:1

SOS

Automated de novo transcriptome assembly

Language:PythonStargazers:3Issues:3Issues:3