Alternatives and similar repositories for pipeline

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

• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆67Updated last year
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆72Updated 2 years ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 4 years ago
• hsgweon / pipits
  Automated pipeline for analyses of fungal ITS from the Illumina
  ☆31Updated 3 months ago
• pr2database / pr2database
  Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
  ☆82Updated last month
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 2 years ago
• agmcfarland / r_phylogenetics_worshop
  Using ggtree to build phylogenetic trees
  ☆47Updated 9 months ago
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆90Updated this week
• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆87Updated last year
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆30Updated 5 years ago
• Zymo-Research / figaro
  An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
  ☆90Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆46Updated 5 years ago
• MadsAlbertsen / multi-metagenome
  Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
  ☆81Updated 9 years ago
• geronimp / graftM
  GraftM - Rapid community profiles from metagenomes
  ☆46Updated last year
• treangenlab / emu
  ☆57Updated 2 weeks ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆109Updated 3 months ago
• terrimporter / CO1Classifier
  This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequen…
  ☆32Updated 2 years ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆56Updated 3 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆55Updated last year
• alipirani88 / Comparative_Genomics
  Micro 612 genomics workshop
  ☆37Updated 4 years ago
• frederic-mahe / swarm
  A robust and fast clustering method for amplicon-based studies
  ☆31Updated 2 years ago
• mikerobeson / make_SILVA_db
  General procedure for making QIIME 2 compatible SILVA reference files
  ☆20Updated 10 months ago
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆103Updated 6 months ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆54Updated 3 years ago
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆126Updated last month
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆28Updated 6 months ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• ddarriba / jmodeltest2
  Automatically exported from code.google.com/p/jmodeltest2
  ☆80Updated 3 years ago
• AntonelliLab / seqcap_processor
  Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics
  ☆21Updated 2 years ago