Alternatives and similar repositories for card-krakendb:

Users that are interested in card-krakendb are comparing it to the libraries listed below

• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• SilvioWeging / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated last year
• aesheppard / TETyper
  transposable element typing pipeline
  ☆17Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆18Updated 6 months ago
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆29Updated 2 weeks ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago
• janepipistrelle / bacterial_GWAS_tutorial
  Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
  ☆18Updated 9 years ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• nf-core / pathogensurveillance
  Surveillance of pathogens using population genomics and sequencing
  ☆22Updated this week
• sanger-pathogens / panito
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Updated 6 years ago
• ktrappe / daisy
  Horizontal Gene Transfer Detection by Mapping Sequencing Reads
  ☆21Updated 7 years ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 6 months ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• zheminzhou / SPARSE
  Strain Prediction and Analysis with Representative SEquence
  ☆18Updated 4 months ago
• colindaven / guppy_on_slurm
  Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
  ☆16Updated 9 months ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• ProwlerForNanopore / ProwlerTrimmer
  Trimming tool for Oxford Nanopore sequence data
  ☆21Updated 3 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆21Updated 7 months ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 6 years ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated last year
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 2 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 6 months ago
• tseemann / mokka
  Annotate your metagenome assemblies
  ☆11Updated 6 years ago
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 4 months ago