Alternatives and similar repositories for microbiome_helper

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

• picrust / picrust2
  Code, unit tests, and tutorials for running PICRUSt2
  ☆364Updated 3 months ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆422Updated 3 weeks ago
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆434Updated 2 years ago
• biobakery / biobakery
  bioBakery tools for meta'omic profiling
  ☆285Updated 2 months ago
• taowenmicro / EasyMicrobiomeR
  Using R language in microbiome analysis
  ☆335Updated 2 years ago
• benjjneb / dada2
  Accurate sample inference from amplicon data with single nucleotide resolution
  ☆515Updated 3 weeks ago
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆534Updated last year
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆421Updated 10 months ago
• YongxinLiu / EasyAmplicon
  Easy Amplicon data analysis pipeline
  ☆310Updated last week
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆358Updated last month
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆347Updated last week
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆519Updated 4 months ago
• nf-core / ampliseq
  Amplicon sequencing analysis workflow using DADA2 and QIIME2
  ☆212Updated 2 weeks ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆379Updated last month
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆354Updated 3 years ago
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆387Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆296Updated 10 months ago
• shenwei356 / taxonkit
  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
  ☆430Updated 3 months ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆379Updated last week
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆605Updated last year
• qiime2 / qiime2
  Source for the QIIME 2 Framework (Q2F).
  ☆510Updated last week
• thackl / gggenomes
  A grammar of graphics for comparative genomics
  ☆690Updated last month
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆239Updated 4 years ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆518Updated last week
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆394Updated 3 months ago
• YongxinLiu / EasyMetagenome
  Easy Metagenome Pipeline
  ☆459Updated 2 weeks ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆811Updated 2 weeks ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆640Updated last month
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆466Updated 2 months ago
• ablab / quast
  Genome assembly evaluation tool
  ☆451Updated 8 months ago