Alternatives and similar repositories for pgap

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

• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 6 months ago
• zhaoc1 / nanoflow
  Bioinformatics pipeline for nanopore sequencing data
  ☆11Updated 6 years ago
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆11Updated 6 months ago
• svm-zhang / AGOUTI
  Annotated Genome Optimization Using Transcriptome Information
  ☆19Updated 5 years ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆21Updated 8 months ago
• scwatts / genome_painter
  Paint genomes with taxa-specific k-mer probabilities
  ☆15Updated 3 years ago
• marbl / gingr
  ☆14Updated last year
• alexiswl / poreduck
  A comprehensive toolkit for running Oxford Nanopore's MinION
  ☆12Updated 6 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆29Updated 2 months ago
• Gardner-BinfLab / deltaBS
  Quantifying the significance of genetic variation using probabilistic profile-based methods.
  ☆19Updated 4 years ago
• aindj / k-SLAM
  k-SLAM ultra fast alignment and taxonomic classification of metagenomic datasets
  ☆23Updated 6 years ago
• bede / kindel
  Indel-aware consensus for aligned BAM
  ☆21Updated 2 months ago
• ansariazim / treeBreaker
  Algorithm to divide a phylogenetic tree into segments based on phenotypes at the leaves of the tree
  ☆25Updated 6 years ago
• vice87 / gam-ngs
  Genomic Assemblies Merger for NGS
  ☆26Updated last year
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆25Updated 8 months ago
• TGenNorth / NASP
  Northern Arizona SNP Pipeline
  ☆19Updated 7 months ago
• nf-core / vipr
  Assembly and intrahost / low-frequency variant calling for viral samples
  ☆14Updated 5 years ago
• CAMI-challenge / CAMITAX
  CAMITAX: Taxon labels for microbial genomes
  ☆29Updated last year
• SR-Martin / alvis
  ☆20Updated last year
• COMBINE-lab / RapClust
  Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
  ☆31Updated 11 months ago
• karel-brinda / samsift
  SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.
  ☆23Updated 7 years ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• md5sam / Falcon2Fastg
  Falcon2Fastg is a tool for converting a FALCON assembly to FASTG format to visualize with Bandage
  ☆13Updated 9 years ago
• sanger-pathogens / panito
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Updated 6 years ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 6 years ago
• HadrienG / nanoflow
  De novo assembly of nanopore reads using nextflow
  ☆20Updated 4 years ago
• SwingOlive / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated last year