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Eric Edsinger (000generic)

000generic

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Location:Campeche, Mexico

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Eric Edsinger's starred repositories

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Language:CLicense:NOASSERTIONStargazers:1734Issues:86Issues:1102

sra-tools

SRA Tools

Language:CLicense:NOASSERTIONStargazers:1081Issues:56Issues:836

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

Language:PerlLicense:BSD-3-ClauseStargazers:812Issues:57Issues:1348

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Language:PythonLicense:NOASSERTIONStargazers:743Issues:68Issues:1033

Flye

De novo assembler for single molecule sequencing reads using repeat graphs

Language:CLicense:NOASSERTIONStargazers:739Issues:28Issues:672

kraken2

The second version of the Kraken taxonomic sequence classification system

Language:C++License:MITStargazers:690Issues:30Issues:801

OrthoFinder

Phylogenetic orthology inference for comparative genomics

Language:PythonLicense:GPL-3.0Stargazers:652Issues:27Issues:886

nanopolish

Signal-level algorithms for MinION data

Language:C++License:MITStargazers:551Issues:37Issues:1014

hisat2

Graph-based alignment (Hierarchical Graph FM index)

Language:C++License:GPL-3.0Stargazers:464Issues:38Issues:354

Jellyfish

A fast multi-threaded k-mer counter

Language:C++License:NOASSERTIONStargazers:455Issues:30Issues:182

quast

Genome assembly evaluation tool

Language:AMPLLicense:NOASSERTIONStargazers:379Issues:41Issues:235

pilon

Pilon is an automated genome assembly improvement and variant detection tool

Language:ScalaLicense:GPL-2.0Stargazers:337Issues:30Issues:169

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

Language:C++License:MITStargazers:260Issues:22Issues:233

TransDecoder

TransDecoder source

Language:PerlLicense:NOASSERTIONStargazers:258Issues:17Issues:191

RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

Language:PerlLicense:NOASSERTIONStargazers:217Issues:6Issues:244

quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Language:C++License:GPL-3.0Stargazers:194Issues:12Issues:70

PASApipeline

PASA software

Language:PerlLicense:NOASSERTIONStargazers:168Issues:13Issues:303

taiyaki

Training models for basecalling Oxford Nanopore reads

Language:PythonLicense:NOASSERTIONStargazers:113Issues:40Issues:101

Peregrine

Peregrine: Fast Genome Assembler Using SHIMMER Index

Language:Jupyter NotebookLicense:NOASSERTIONStargazers:99Issues:8Issues:35

pomoxis

Analysis components from Oxford Nanopore Research

Language:PythonLicense:NOASSERTIONStargazers:92Issues:31Issues:41

illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).

Language:PythonLicense:GPL-2.0Stargazers:89Issues:12Issues:20

LoReAn

Long Reads Annotation pipeline

Language:PythonLicense:MITStargazers:70Issues:8Issues:46

helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Language:PythonLicense:MITStargazers:68Issues:6Issues:27

SNAP

Gene prediction software

Language:CLicense:NOASSERTIONStargazers:59Issues:7Issues:18

MarginPolish

MarginPolish: Graph based assembly polishing

Language:CLicense:MITStargazers:45Issues:4Issues:14

GenericRepeatFinder

Language:C++License:GPL-3.0Stargazers:34Issues:3Issues:7

transabyss

de novo assembly of RNA-seq data using ABySS

Language:PythonLicense:NOASSERTIONStargazers:33Issues:20Issues:29

Apollo

Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described in the Bioinformatics journal paper (2020) by Firtina et al. at https://people.inf.ethz.ch/omutlu/pub/apollo-technology-independent-genome-assembly-polishing_bioinformatics20.pdf

Language:C++License:GPL-3.0Stargazers:27Issues:5Issues:7

OrthoMCL

Language:PerlStargazers:24Issues:12Issues:10

CARP

Correlative Algorithm for Repeat Placement

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