pha4ge / pipeline-resources

Related projects: ⓘ

• 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…
  ☆35Updated 2 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆75Updated 2 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆42Updated 4 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆89Updated last week
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆55Updated this week
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆105Updated 3 months ago
• CDCgov / datasets-sars-cov-2
  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
  ☆54Updated last year
• adlape95 / Assembly-methods-nanopore
  Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  ☆18Updated 4 years ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆68Updated last month
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆47Updated this week
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆53Updated 3 years ago
• lmrodriguezr / enveomics
  Scripts and libraries for Environmental Genomics
  ☆37Updated 7 months ago
• marbl / harvest
  ☆51Updated 3 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆46Updated last year
• klebgenomics / Kaptive
  ☆43Updated 2 months ago
• CDCgov / mycosnp-nf
  CDCgov/mycosnp-nf
  ☆36Updated last week
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆69Updated last year
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆32Updated this week
• jhawkey / IS_mapper
  IS mapping software
  ☆50Updated 2 years ago
• treangenlab / emu
  ☆31Updated 2 weeks ago
• UPHL-BioNGS / Cecret
  Reference-based consensus creation
  ☆48Updated last week
• simonrharris / SKA
  Split Kmer Analysis
  ☆62Updated 2 years ago
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆42Updated 5 months ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆70Updated 9 months ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆34Updated 9 months ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆50Updated 3 weeks ago
• jodyphelan / tbdb
  Standard database for the TBProfiler tool
  ☆28Updated 3 weeks ago
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆16Updated last year
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆27Updated last year
• 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