Alternatives and similar repositories for illumina-utils

Users that are interested in illumina-utils are comparing it to the libraries listed below

• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 5 months ago
• schmeing / ReSeq
  More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original
  ☆52Updated 2 years ago
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆94Updated last month
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆54Updated 3 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated last year
• mw55309 / Kraken_db_install_scripts
  Updated Kraken DB install scripts to cope with new-ish NCBI structure
  ☆46Updated 8 years ago
• edamame-course / Metagenome
  ☆23Updated 6 years ago
• grenaud / deML
  Maximum likelihood demultiplexing
  ☆47Updated 3 months ago
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆45Updated 5 years 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…
  ☆54Updated 3 years ago
• ridgelab / JustOrthologs
  ☆35Updated 2 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆71Updated 3 years ago
• frankMusacchia / Annocript
  Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved …
  ☆55Updated 5 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆57Updated last year
• fbreitwieser / bamcov
  Quickly calculate and visualize sequence coverage in alignment files
  ☆99Updated 5 years ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆61Updated last year
• MVesuviusC / primerTree
  PrimerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs
  ☆52Updated last year
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆66Updated last year
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆67Updated 4 years ago
• sujaikumar / assemblage
  Tools for working with second gen assemblies, fasta sequences, etc
  ☆93Updated 8 years ago
• rrwick / Metagenomics-Index-Correction
  ☆82Updated last year
• pachterlab / metakallisto
  Using kallisto for metagenomic analysis
  ☆50Updated 8 years ago
• calacademy-research / minibar
  Dual barcode and primer demultiplexing for MinION sequenced reads
  ☆39Updated 2 years ago
• sanger-pathogens / pathogen-informatics-training
  ☆70Updated 4 years ago
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆67Updated 7 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• CSB5 / lofreq
  LoFreq Star: Sensitive variant calling from sequencing data
  ☆105Updated 2 years ago
• Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis
  Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
  ☆32Updated 2 years ago
• caporaso-lab / mockrobiota
  A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.
  ☆81Updated 6 years ago