Alternatives and similar repositories for siamcat:

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

• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 2 months ago
• cafferychen777 / MicrobiomeStat
  Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
  ☆40Updated last month
• biobakery / maaslin3
  MaAsLin3: Microbiome Multivariate Association with Linear Models
  ☆33Updated last week
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆33Updated 4 years ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆51Updated 3 years ago
• victoriapascal / gutsmash
  gutSMASH
  ☆53Updated 3 months ago
• EnvGen / metagenomics-workshop
  Metagenomics Workshop
  ☆28Updated 8 years ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis
  Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
  ☆27Updated last year
• Finn-Lab / MGS-gut
  Analysing Metagenomic Species (MGS)
  ☆41Updated 4 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 3 months ago
• wdl2459 / ConQuR
  Batch effects removal for microbiome data via conditional quantile regression
  ☆27Updated 2 years ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated last year
• microUCPH / amplicon_data_analysis
  Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project
  ☆11Updated 2 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
  ☆55Updated 6 months ago
• knightlab-analyses / reference-frames
  ☆20Updated 4 years ago
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆73Updated last week
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆44Updated 4 years ago
• SegataLab / metamlst
  MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
  ☆14Updated 2 years ago
• biobakery / melonnpan
  Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
  ☆35Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated last year
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated 10 months 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…
  ☆52Updated 3 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• jlw-ecoevo / gRodon
  ☆17Updated 2 years ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆24Updated 5 months ago
• zellerlab / crc_meta
  Code and analysis results for the CRC shotgun meta-analysis
  ☆38Updated 2 years ago
• waldronlab / curatedMetagenomicDataAnalyses
  Analyses in R and Python Using curatedMetagenomicData
  ☆29Updated 2 months ago