Alternatives and similar repositories for gappa

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

• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆86Updated 3 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆51Updated 3 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆72Updated 4 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆61Updated 2 years ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 6 months ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆34Updated last year
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆71Updated 5 years ago
• ctmrbio / stag-mwc
  StaG Metagenomic Workflow Collaboration
  ☆28Updated last year
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• BenoitMorel / ParGenes
  A massively parallel tool for model selection and tree inference on thousands of genes
  ☆51Updated last year
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆25Updated last year
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆68Updated 3 years ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆93Updated 3 weeks ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆74Updated 4 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆96Updated 3 months ago
• stajichlab / AAFTF
  Automatic Assembly For The Fungi
  ☆25Updated 3 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆64Updated 3 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆87Updated 3 years ago
• rrwick / Metagenomics-Index-Correction
  ☆84Updated 2 years ago
• thackl / minidot
  Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
  ☆77Updated 9 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 3 years ago
• geronimp / graftM
  GraftM - Rapid community profiles from metagenomes
  ☆47Updated last month
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆64Updated 6 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 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
  ☆66Updated last year
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆73Updated 6 years ago