Alternatives and similar repositories for metaseek

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

• sourmash-bio / databases

  View on GitHub
  Build sourmash databases for genbank.
  ☆11May 4, 2023Updated 2 years ago
• epruesse / ymp

  View on GitHub
  Flexible omics pipeline
  ☆17Oct 16, 2025Updated 4 months ago
• brainstorm / s3-rust-htslib-bam

  View on GitHub
  AWS lambda S3 + rust-htslib: A serverless bioinformatics example
  ☆14Jun 7, 2022Updated 3 years ago
• sckott / pytaxa

  View on GitHub
  taxonomic classes for Python
  ☆11Aug 30, 2021Updated 4 years ago
• LiuBioinfo / SeqOthello

  View on GitHub
  SeqOthello supports fast coverage query and containment query.
  ☆12May 8, 2019Updated 6 years ago
• St4NNi / jam-rs

  View on GitHub
  Just another minhash implementation.
  ☆12Updated this week
• ababaian / palmid

  View on GitHub
  RNA dependent RNA Polymerase Palmprint Analysis
  ☆12Aug 1, 2024Updated last year
• Arcadia-Science / sourmashconsumr

  View on GitHub
  Working with the outputs of sourmash in R
  ☆28Jan 15, 2026Updated last month
• dib-lab / 2018-ncbi-lineages

  View on GitHub
  Extract lineage CSVs from NCBI for use with sourmash lca.
  ☆29Oct 4, 2023Updated 2 years ago
• linsalrob / partie

  View on GitHub
  PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…
  ☆25Feb 25, 2023Updated 2 years ago
• dib-lab / elvers

  View on GitHub
  (formerly eelpond) an automated RNA-Seq workflow system
  ☆27Oct 14, 2020Updated 5 years ago
• statdivlab / groves

  View on GitHub
  Tools for analyzing trees
  ☆13Apr 16, 2025Updated 10 months ago
• sourmash-bio / branchwater

  View on GitHub
  Searching large collections of sequencing data with genome-scale queries
  ☆16Feb 5, 2026Updated last week
• lmlui / Jorg

  View on GitHub
  MAG Circularization Method
  ☆32Nov 4, 2025Updated 3 months ago
• ngs-docs / 2018-cicese-metatranscriptomics

  View on GitHub
  repo for cicese metatranscriptomics workshop, nov 2018
  ☆14Jan 22, 2020Updated 6 years ago
• ggloor / compositions

  View on GitHub
  Site that contains musings and code for compositional analysis of high throughput sequencing experiments
  ☆17Apr 18, 2024Updated last year
• sourmash-bio / wort

  View on GitHub
  A database for signatures of public genomic sources
  ☆18Jan 1, 2026Updated last month
• SamStudio8 / hansel

  View on GitHub
  A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence
  ☆17Jun 29, 2021Updated 4 years ago
• sourmash-bio / mastiff

  View on GitHub
  ☆16Jan 21, 2024Updated 2 years ago
• spacegraphcats / spacegraphcats

  View on GitHub
  Indexing & querying large assembly graphs -- in space, no one can hear you miao!
  ☆118Jan 29, 2026Updated 2 weeks ago
• borenstein-lab / burrito

  View on GitHub
  A visualization tool for exploratory data analysis of metagenomic data
  ☆39Mar 22, 2022Updated 3 years ago
• PNNL-CompBio / Snekmer

  View on GitHub
  Pipeline to apply encoded Kmer analysis to protein sequences
  ☆16Feb 2, 2026Updated 2 weeks ago
• linsalrob / SRA_Metadata

  View on GitHub
  Get, parse, and extract information from the SRA metadata files
  ☆46Sep 20, 2022Updated 3 years ago
• COMBINE-lab / kmers

  View on GitHub
  A bit-packed k-mer representation (and relevant utilities) for rust
  ☆47Jun 26, 2024Updated last year
• dahak-metagenomics / dahak

  View on GitHub
  benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
  ☆21Sep 21, 2018Updated 7 years ago
• dib-lab / dib-MMETSP

  View on GitHub
  Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)
  ☆23Apr 14, 2019Updated 6 years ago
• soedinglab / WIsH

  View on GitHub
  Predict prokaryotic host for phage metagenomic sequences
  ☆54Sep 17, 2024Updated last year
• niemasd / ViralConsensus

  View on GitHub
  Fast viral consensus genome reconstruction
  ☆25Feb 5, 2026Updated last week
• ewissel / hAMRoaster

  View on GitHub
  hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
  ☆22Mar 8, 2024Updated last year
• dib-lab / charcoal

  View on GitHub
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Nov 3, 2023Updated 2 years ago
• nick-youngblut / traitar3

  View on GitHub
  From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)
  ☆21Jul 8, 2024Updated last year
• pgxcentre / manhattan_generator

  View on GitHub
  Manhattan plot Generator
  ☆24Jun 1, 2020Updated 5 years ago
• sourmash-bio / sourmash_plugin_branchwater

  View on GitHub
  fast, multithreaded sourmash operations: search, compare, and gather.
  ☆25Feb 9, 2026Updated last week
• Gibbons-Lab / isb_course_2022

  View on GitHub
  Materials and presentation for the 2022 ISB Microbiome course.
  ☆27Jun 13, 2024Updated last year
• genomicepidemiology / ARGprofiler

  View on GitHub
  A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
  ☆31Nov 9, 2025Updated 3 months ago
• rcedgar / palmscan

  View on GitHub
  ☆26Jun 26, 2025Updated 7 months ago
• will-rowe / hulk

  View on GitHub
  Histosketching Using Little Kmers
  ☆56May 25, 2023Updated 2 years ago
• qiyunlab / binarena

  View on GitHub
  BinaRena: Interactive Visualization and Binning of Metagenomic Contigs
  ☆33Aug 22, 2024Updated last year
• greenelab / adage

  View on GitHub
  Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · …
  ☆61May 26, 2016Updated 9 years ago