Alternatives and similar repositories for pipelines

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

• iqbal-lab / Mykrobe-predictor
  Antibiotic resistance predictions in minutes on a laptop
  ☆50Updated 6 years ago
• linsalrob / partie
  PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…
  ☆26Updated 2 years ago
• WGS-standards-and-analysis / datasets
  Benchmark datasets for WGS analysis
  ☆39Updated 5 years ago
• dahak-metagenomics / dahak
  benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
  ☆21Updated 6 years ago
• ncbi / rapt
  This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
  ☆58Updated 3 months ago
• karel-brinda / ococo
  Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
  ☆47Updated 6 years ago
• CAMI-challenge / OPAL
  OPAL: Open-community Profiling Assessment tooL
  ☆29Updated 6 months ago
• ktmeaton / NCBImeta
  Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).
  ☆49Updated 3 years ago
• nickloman / poredb
  ☆19Updated 8 years ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 6 years ago
• snayfach / IGGsearch
  Metagenomic species profiling with enhanced coverage of the human gut microbiome
  ☆25Updated last year
• phac-nml / biohansel
  Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
  ☆28Updated 7 months ago
• kdm9 / kWIP
  De novo estimates of genetic relatedness from next-gen sequencing data
  ☆45Updated 5 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• blaxterlab / blobology
  Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a …
  ☆46Updated 3 years ago
• sestaton / Transposome
  A toolkit for annotation of transposable element families from unassembled sequence reads
  ☆30Updated 2 years ago
• jts / nanopore-paper-analysis
  Code for nanopore paper
  ☆33Updated 10 years ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆30Updated 2 years ago
• merenlab / reads-for-assembly
  Simulate metagenomic short reads from one or more populations.
  ☆26Updated 5 months ago
• sharpton / shotmap
  A Shotgun Metagenome Annotation Pipeline
  ☆23Updated 8 years ago
• jaleezyy / covid-19-signal
  Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
  ☆31Updated 6 months ago
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆56Updated 4 years ago
• naturalis / wgs2ncbi
  Toolkit for preparing genomes for submission to NCBI
  ☆30Updated 3 years ago
• pirovc / metameta
  ☆23Updated 5 years ago
• NCBI-Hackathons / NovoGraph
  NovoGraph: building whole genome graphs from long-read-based de novo assemblies
  ☆45Updated 4 years ago
• dkoslicki / MetaPalette
  Metagenomic profiling and phylogenetic distances via common kmers
  ☆42Updated 4 years ago
• geraldinepascal / FROGS
  FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data.
  ☆31Updated 2 months ago
• rrwick / Catpac
  a Contig Alignment Tool for Pairwise Assembly Comparison
  ☆13Updated 5 years ago
• merenlab / MerenLab-workflows
  A repository with scripts to run pipeline that are commonly used in the Meren Lab
  ☆11Updated 7 years ago
• iqbal-lab-org / clockwork
  CRyPTIC data processing pipelines
  ☆34Updated 11 months ago