Jolvii85

Jolvii85's Stars

• marcomilanesi/BITE

  BITE: BioInformatics tools for everyone

  199

• RasmussenLab/vamb

  Variational autoencoder for metagenomic binning

  Language:Python26247

• nf-core/mag

  Assembly and binning of metagenomes

  Language:Nextflow217110

• millanek/Dsuite

  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

  Language:C++16225

• Nextomics/NextDenovo

  Fast and accurate de novo assembler for long reads

  Language:C37053

• songweizhi/MetaCHIP

  Horizontal gene transfer (HGT) identification pipeline

  Language:Python5614

• Ecogenomics/GTDBTk

  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

  Language:Python47982

• broadinstitute/gatk

  Official code repository for GATK versions 4 and up

  Language:Java1.7k594

• bxlab/metaWRAP

  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

  Language:Shell399190

• xiaoming-liu/stairway-plot-v2

  The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data.

  Language:Java314

• ksamuk/pixy

  Software for painlessly estimating average nucleotide diversity within and between populations

  Language:Python12014

• speciationgenomics/scripts

  Scripts for analysis used during the course

  Language:R8262

• isaacovercast/easySFS

  Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis

  Language:Python13624

• mmatschiner/tutorials

  Tutorials on phylogenetic and phylogenomic inference

  Language:HTML367170

• FerRacimo/GRoSS

  Graph-aware Retrieval of Selective Sweeps

  Language:R215

• aidenlab/Juicebox

  Visualization and analysis software for Hi-C data -

  Language:Java24558

• aidenlab/3d-dna

  3D de novo assembly (3D DNA) pipeline

  Language:Shell20755

• russcd/vcf2MK

  Language:C++6

• Dfam-consortium/RepeatMasker

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

  Language:Perl23149

• coreutils/coreutils

  upstream mirror

  Language:C4.3k930

• aidenlab/juicer

  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

  Language:Shell418183

• tanghaibao/goatools

  Python library to handle Gene Ontology (GO) terms

  Language:Python782210

• bcgsc/ntEdit

  ✏️ Genome assembly polishing & SNV detection

  Language:C++649

• panammeb/PANAM2

  PANAM2 is a pipeline for depicting the microbial community by implementing a phylogenetic approach for the annotation of the gene coding for 16S and 18S rRNA. It is based on PANAM (Taib et al. 2013) with some improvements and focusing on Illumina sequencing.

  Language:Perl22

• holtjma/fmlrc

  a long-read error correction tool using the multi-string Burrows Wheeler Transform

  Language:C++463

• ruanjue/smartdenovo

  Ultra-fast de novo assembler using long noisy reads

  Language:C13030

• ruanjue/wtdbg2

  Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

  Language:C51394

• broadinstitute/pilon

  Pilon is an automated genome assembly improvement and variant detection tool

  Language:Scala34160

• marbl/canu

  A single molecule sequence assembler for genomes large and small.

  Language:C++660179