Alternatives and similar repositories for SCRuB

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

• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆32Updated last month
• ivlachos / agamemnon
  Accurate metagenomi/metatranscriptomic analysis pipeline
  ☆23Updated 4 years ago
• biobakery / shortbred
  ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then sear…
  ☆32Updated 7 months ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆61Updated last year
• victoriapascal / gutsmash
  gutSMASH
  ☆55Updated 8 months ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆54Updated 2 months ago
• ParkinsonLab / MetaPro
  ☆22Updated last week
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆73Updated 5 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
• bhattlab / phanta
  Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
  ☆65Updated last month
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• ngs-docs / 2018-cicese-metatranscriptomics
  repo for cicese metatranscriptomics workshop, nov 2018
  ☆14Updated 5 years ago
• blekhmanlab / biomehorizon
  Plot microbiome time series in parallel
  ☆26Updated last year
• danielpodlesny / samestr
  SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.
  ☆24Updated 3 weeks ago
• biobakery / maaslin3
  MaAsLin3: Microbiome Multivariate Association with Linear Models
  ☆43Updated this week
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆29Updated 8 months ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated 2 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• hoelzer / pocp
  Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.
  ☆26Updated 4 months ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆63Updated 2 months ago
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆36Updated 10 months ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆46Updated 5 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆68Updated last week
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆54Updated 5 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆65Updated 2 years ago
• balabanmetin / uDance
  ☆42Updated last year
• pollardlab / MIDAS
  Metagenomic Intra-Species Diversity Analysis (MIDAS)
  ☆40Updated 11 months ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆49Updated this week
• wdl2459 / ConQuR
  Batch effects removal for microbiome data via conditional quantile regression
  ☆31Updated 3 years ago