Alternatives and similar repositories for biom-format

Users that are interested in biom-format are comparing it to the libraries listed below

• mgalardini / pyseer
  SEER, reimplemented in python 🐍🔮
  ☆128Updated 8 months ago
• fhcrc / seqmagick
  An imagemagick-like frontend to Biopython SeqIO
  ☆117Updated last year
• biocore / redbiom
  Sample search by metadata and features
  ☆47Updated 2 years ago
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆129Updated last year
• snayfach / MIDAS
  An integrated pipeline for estimating strain-level genomic variation from metagenomic data
  ☆132Updated 2 years ago
• chiulab / surpi
  SURPI
  ☆86Updated 9 years ago
• husonlab / megan-ce
  MEGAN Community Edition
  ☆72Updated last year
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆99Updated 3 weeks ago
• merenlab / illumina-utils
  A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
  ☆94Updated 2 months ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆65Updated 6 years ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆151Updated 3 weeks ago
• biocore / songbird
  Vanilla regression methods for microbiome differential abundance analysis
  ☆60Updated 5 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated 2 years ago
• flexidot-bio / flexidot
  Highly customizable, ambiguity-aware dotplots for visual sequence analyses
  ☆99Updated this week
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆123Updated 3 weeks ago
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆58Updated 4 years ago
• qiyunzhu / woltka
  Woltka: a versatile meta'omic data classifier
  ☆76Updated 4 months ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• genotoul-bioinfo / dgenies
  Dotplot large Genomes in an Interactive, Efficient and Simple way
  ☆112Updated last week
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆61Updated last year
• nick-youngblut / gtdb_to_taxdump
  Convert GTDB taxonomy to NCBI taxdump format
  ☆74Updated 2 years ago
• FOI-Bioinformatics / flextaxd
  FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…
  ☆67Updated 10 months ago
• epruesse / SINA
  SINA - Reference based multiple sequence alignment
  ☆41Updated 5 years ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• csmiller / EMIRGE
  EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
  ☆38Updated 2 years ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆83Updated 4 months ago
• PathoScope / PathoScope
  Pathoscope: Species identification and strain attribution with unassembled sequencing data
  ☆60Updated 6 years ago
• sanger-pathogens / pathogen-informatics-training
  ☆76Updated 5 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆119Updated last year
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆100Updated 3 years ago