Alternatives and similar repositories for BACTpipe

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

• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆24Updated 2 years ago
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆24Updated 2 months ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 3 years ago
• FredHutch / nf-anvio-pangenome
  Analyze a set of genomes with the anvi'o pangenome pipeline
  ☆16Updated 2 years ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆39Updated 9 months ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆12Updated last year
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• moshi4 / plot_genome_align_fig
  Plot genome alignment figure using progressiveMauve & genoPlotR
  ☆22Updated 3 years ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 3 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 6 years ago
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated 2 years ago
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆24Updated 2 years ago
• nf-core / bactmap
  A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
  ☆60Updated 3 weeks ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆20Updated 2 weeks ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 9 months ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆23Updated last year
• farhat-lab / fast-lineage-caller
  ☆14Updated 4 years ago
• phac-nml / neptune
  Neptune: Genomic Signature Discovery
  ☆20Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 6 years ago
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆25Updated 2 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆11Updated last year
• klebgenomics / Kleborate-viz
  Visualisation application for Klebsiella genotypes generated by Kleborate.
  ☆10Updated 2 months ago
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆45Updated last week