MicrobeLab / DeepMicrobes

Related projects ⓘ

Alternatives and complementary repositories for DeepMicrobes

• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated last year
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆110Updated last year
• nick-youngblut / gtdb_to_taxdump
  Convert GTDB taxonomy to NCBI taxdump format
  ☆66Updated last year
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆68Updated 4 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆70Updated last year
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆56Updated 7 months ago
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆191Updated 2 weeks ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆78Updated last month
• snayfach / MGV
  Supporting code for uncultivated gut virus manuscript
  ☆66Updated last year
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆61Updated this week
• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆55Updated last year
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆109Updated 6 months ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆47Updated 2 years ago
• scwatts / fastspar
  Rapid and scalable correlation estimation for compositional data
  ☆79Updated 6 months ago
• qiyunzhu / woltka
  Woltka: a versatile meta'omic data classifier
  ☆70Updated last month
• EBI-Metagenomics / genomes-catalogue-pipeline
  MGnify genome analysis pipeline
  ☆101Updated this week
• ohmeta / metapi
  A general metagenomics data mining system focus on robust microbiome research
  ☆56Updated 2 months ago
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆67Updated 2 years ago
• AstrobioMike / bit
  Bioinformatics Tools
  ☆81Updated 3 weeks ago
• hzi-bifo / RiboDetector
  Accurate and rapid RiboRNA sequences Detector based on deep learning
  ☆99Updated 10 months ago
• mdsufz / MuDoGeR
  MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
  ☆87Updated 3 months ago
• Finn-Lab / MGS-gut
  Analysing Metagenomic Species (MGS)
  ☆41Updated 4 years ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆67Updated 8 months ago
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆147Updated 6 months ago
• snayfach / MIDAS
  An integrated pipeline for estimating strain-level genomic variation from metagenomic data
  ☆124Updated last year
• rrwick / Metagenomics-Index-Correction
  ☆79Updated last year
• biobakery / kneaddata
  Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
  ☆107Updated this week
• Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis
  Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
  ☆26Updated last year
• marbl / parsnp
  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…
  ☆129Updated this week
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 3 years ago