Alternatives and similar repositories for biobakery_workflows:

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

• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆60Updated last year
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆114Updated 9 months ago
• biobakery / kneaddata
  Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
  ☆114Updated this week
• biobakery / Maaslin2
  MaAsLin2: Microbiome Multivariate Association with Linear Models
  ☆131Updated 3 months ago
• benjjneb / decontam
  Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
  ☆153Updated last year
• SegataLab / lefse
  ☆83Updated 8 months ago
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆208Updated last month
• cafferychen777 / ggpicrust2
  Make Picrust2 Output Analysis and Visualization Easier
  ☆120Updated 2 weeks ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆115Updated last year
• YongxinLiu / Metagenome
  Metagenome analysis pipeline
  ☆94Updated 3 years ago
• MaestSi / MetONTIIME
  A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
  ☆91Updated 8 months ago
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆202Updated 2 months ago
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆159Updated 9 months ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆140Updated this week
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆204Updated last week
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆136Updated this week
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆111Updated last month
• mgoeker / table2itol
  Generating iToL annotations from Spreadsheet or CSV files
  ☆97Updated 4 years ago
• chklovski / CheckM2
  Assessing the quality of metagenome-derived genome bins using machine learning
  ☆195Updated last week
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆74Updated this week
• cmks / DAS_Tool
  DAS Tool
  ☆146Updated 9 months ago
• biobakery / humann
  HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
  ☆184Updated 5 months ago
• cruizperez / MicrobeAnnotator
  Pipeline for metabolic annotation of microbial genomes
  ☆142Updated 7 months ago
• donovan-h-parks / STAMP
  Statistical Analysis of Metagenomic Profiles
  ☆93Updated 5 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆57Updated 10 months ago
• xia-lab / MicrobiomeAnalystR
  A companion R package for the MicrobiomeAnalyst web server
  ☆120Updated last month
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆66Updated this week
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆137Updated last year
• Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis
  Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
  ☆27Updated last year
• linnabrown / run_dbcan
  Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for…
  ☆149Updated 3 weeks ago