Alternatives and similar repositories for pipeline-resources

Users that are interested in pipeline-resources are comparing it to the libraries listed below

• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆47Updated 5 years ago
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆41Updated last year
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆36Updated 3 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated 2 weeks ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• lmrodriguezr / enveomics
  Scripts and libraries for Environmental Genomics
  ☆38Updated 6 months ago
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆75Updated last year
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆63Updated 11 months ago
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆17Updated 2 years ago
• theiagen / public_health_bioinformatics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…
  ☆55Updated last week
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆37Updated 2 months ago
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆56Updated 4 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆29Updated 8 months ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆66Updated 3 months ago
• bede / hostile
  Precise host read removal
  ☆103Updated 2 months ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆46Updated 2 months ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆67Updated last week
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 4 months ago
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆48Updated last year
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• EBI-Metagenomics / mettannotator
  ☆75Updated this week
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated last year
• UPHL-BioNGS / Cecret
  Reference-based consensus creation
  ☆56Updated last week
• ngs-fzb / MTBseq_source
  MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…
  ☆46Updated last year
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆50Updated 7 months ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆88Updated last month
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆76Updated 2 years ago