Alternatives and similar repositories for CAP2

Users that are interested in CAP2 are comparing it to the libraries listed below

• MetaSUB / MetaSUB_CAP
  A comprehensive pipeline for short read metagenomic data
  ☆25Updated 5 years ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆66Updated last year
• MadsAlbertsen / mmgenome
  Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
  ☆27Updated 8 years ago
• microsud / microbiomeutilities
  The is mostly a wrapper tool using phyloseq and microbiome R packages.
  ☆33Updated 3 years ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• EnvGen / metagenomics-workshop
  Metagenomics Workshop
  ☆28Updated 9 years ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• Microbial-Ecology-Group / AMRplusplus
  AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…
  ☆46Updated 2 weeks ago
• janepipistrelle / bacterial_GWAS_tutorial
  Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
  ☆18Updated 9 years ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆33Updated 5 years ago
• aomlomics / tourmaline
  Amplicon sequence processing workflow using QIIME 2 and Snakemake
  ☆46Updated 2 weeks ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆47Updated 5 years ago
• ctmrbio / stag-mwc
  StaG Metagenomic Workflow Collaboration
  ☆28Updated last year
• snayfach / IGGdb
  Database of genomes integrated from the gut microbiome and other environments
  ☆45Updated 2 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆54Updated 5 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆55Updated 6 months ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆71Updated last year
• sanger-pathogens / mlst_check
  Multilocus sequence typing by blast using the schemes from PubMLST
  ☆30Updated 3 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆51Updated 3 years ago
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆78Updated 5 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆61Updated 2 years ago
• borenstein-lab / fishtaco
  FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…
  ☆24Updated 4 years ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆60Updated last year
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆25Updated last year
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆39Updated 2 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆73Updated 6 years ago
• snayfach / IGGsearch
  Metagenomic species profiling with enhanced coverage of the human gut microbiome
  ☆25Updated last year