Alternatives and similar repositories for baltic

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

• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆161Updated last month
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆123Updated last year
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆116Updated 3 months ago
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆173Updated last month
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆128Updated last month
• BenoitMorel / GeneRax
  ☆71Updated 3 weeks ago
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆103Updated 4 months ago
• fhcrc / seqmagick
  An imagemagick-like frontend to Biopython SeqIO
  ☆115Updated last year
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆147Updated this week
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆74Updated 2 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated last year
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆105Updated last month
• bokulich-lab / RESCRIPt
  REference Sequence annotation and CuRatIon Pipeline
  ☆99Updated this week
• phac-nml / mob-suite
  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  ☆151Updated 2 months ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆99Updated this week
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆231Updated 3 months ago
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆193Updated 2 months ago
• cruizperez / MicrobeAnnotator
  Pipeline for metabolic annotation of microbial genomes
  ☆149Updated 3 months ago
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆85Updated last month
• neherlab / treetime
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
  ☆242Updated 2 weeks ago
• mgalardini / pyseer
  SEER, reimplemented in python 🐍🔮
  ☆122Updated last month
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 2 years ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆121Updated last year
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆71Updated last year
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆97Updated 2 years ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆79Updated last month
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆304Updated 3 months ago
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆147Updated this week
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆76Updated 2 months ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆137Updated last year