ukhsa-collaboration / PHEnix

Related projects ⓘ

Alternatives and complementary repositories for PHEnix

• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 5 years ago
• thackl / minidot
  Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
  ☆74Updated 8 years ago
• cboursnell / transfuse
  Merge transcriptome assemblies
  ☆30Updated 8 years ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆28Updated 6 years ago
• lbcb-sci / ra
  Assembler for raw de novo genome assembly of long uncorrected reads.
  ☆37Updated 4 years ago
• janepipistrelle / bacterial_GWAS_tutorial
  Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
  ☆19Updated 8 years ago
• ibest / ARC
  Assembly by Reduced Complexity (ARC)
  ☆41Updated 8 years ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆56Updated 2 years ago
• nanoporetech / ont_tutorial_basicqc
  A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt
  ☆30Updated 3 years ago
• jbelyeu / SV-plaudit
  Pipeline for structural variant image curation and analysis.
  ☆48Updated 2 years ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆29Updated 3 years ago
• arq5x / nanopore-scripts
  Various scripts and recipes for working with nanopore data
  ☆34Updated 8 years ago
• edamame-course / Metagenome
  ☆23Updated 6 years ago
• katholt / RedDog
  ☆33Updated 2 years ago
• eclarke / swga
  Select primer sets for selective whole genome amplification (SWGA)
  ☆32Updated 5 years ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆45Updated 5 years ago
• institut-de-genomique / NaS
  NaS is a hybrid approach developped to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore tech…
  ☆15Updated 7 years ago
• z0on / GO_MWU
  Rank-based Gene Ontology analysis of gene expression data
  ☆39Updated last year
• dkoslicki / MetaPalette
  Metagenomic profiling and phylogenetic distances via common kmers
  ☆42Updated 3 years ago
• eclarke / komplexity
  A method of assessing sequence complexity based on kmer frequencies
  ☆28Updated 6 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆52Updated last year
• pachterlab / metakallisto
  Using kallisto for metagenomic analysis
  ☆50Updated 7 years ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆32Updated this week
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 3 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 2 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆44Updated last year
• conchoecia / pauvre
  Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.
  ☆52Updated this week
• marbl / VALET
  A pipeline for detecting mis-assemblies in metagenomic assemblies.
  ☆14Updated 7 years ago