Alternatives and similar repositories for pan-genome-analysis

Users that are interested in pan-genome-analysis are comparing it to the libraries listed below

• CompSynBioLab-KoreaUniv / FunGAP
  FunGAP: fungal Genome Annotation Pipeline
  ☆111Updated 2 months ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆100Updated last year
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆140Updated last year
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆164Updated 3 months ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆118Updated 2 months ago
• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆202Updated last year
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆204Updated last year
• sunbeam-labs / sunbeam
  A robust, extensible metagenomics pipeline
  ☆174Updated last week
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆82Updated 3 months ago
• cruizperez / MicrobeAnnotator
  Pipeline for metabolic annotation of microbial genomes
  ☆150Updated 5 months ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated last year
• qiyunlab / HGTector
  HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
  ☆136Updated last year
• CSB5 / OPERA-MS
  OPERA-MS - Hybrid Metagenomic Assembler
  ☆97Updated last year
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆173Updated 4 years ago
• PacificBiosciences / pb-metagenomics-tools
  Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
  ☆193Updated last month
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆106Updated 3 years ago
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆219Updated 3 weeks ago
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆93Updated last week
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆149Updated 3 weeks ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆117Updated 2 years ago
• cmks / DAS_Tool
  DAS Tool
  ☆156Updated last year
• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆63Updated 2 years ago
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆138Updated 3 years ago
• biobakery / phylophlan
  Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
  ☆154Updated 2 months ago
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆172Updated last year
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆219Updated last month
• wdecoster / chopper
  ☆208Updated 3 weeks ago
• BinPro / CONCOCT
  Clustering cONtigs with COverage and ComposiTion
  ☆132Updated 5 years ago
• kblin / ncbi-acc-download
  Download files from NCBI Entrez by accession
  ☆127Updated 11 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆141Updated last month