Alternatives and similar repositories for pafpy

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

• ekg / edyeet
  base-accurate DNA sequence alignments using edlib and mashmap2
  ☆32Updated 4 years ago
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 4 years ago
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated 7 months ago
• PacificBiosciences / portello
  Transfer HiFi read mappings from their own assembly contigs to a standard reference
  ☆28Updated 3 weeks ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆40Updated 2 years ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆29Updated last month
• rcedgar / urmap
  URMAP ultra-fast read mapper
  ☆38Updated 5 years ago
• pierrepeterlongo / back_to_sequences
  ☆45Updated last month
• kcleal / pywfa
  Python wrapper for wavefront alignment using WFA2-lib
  ☆38Updated last year
• nanoporetech / minimappy
  Python bindings to minimap2
  ☆16Updated 8 years ago
• bluenote-1577 / devider
  Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
  ☆39Updated 3 months ago
• jts / bri
  Bam Read Index - Extract alignments from a bam file by readname
  ☆28Updated last year
• kcleal / svbench
  Benchmark structural variant calls against a reference set
  ☆18Updated 2 weeks ago
• pangenome / maffer
  extract MSAs from genome variation graphs
  ☆34Updated 5 years ago
• shenwei356 / wfa
  Wavefront alignment algorithm (WFA) in Golang
  ☆32Updated 5 months ago
• alshai / levioSAM
  Lift-over alignments from variant-aware references
  ☆34Updated 2 years ago
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated 9 months ago
• ACEnglish / kanpig
  Kmer Analysis of Pileups for Genotyping
  ☆35Updated this week
• natir / fpa
  Filter of Pairwise Alignement
  ☆44Updated 3 years ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆24Updated last year
• Parsoa / SVDSS
  Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
  ☆47Updated 4 months ago
• zhixingfeng / iGDA
  Detect and phase minor SNVs from long-read sequencing data
  ☆14Updated 4 years ago
• jltsiren / gbwtgraph
  GBWT-based handle graph
  ☆31Updated this week
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 4 years ago
• benedictpaten / marginPhase
  ☆35Updated 5 years ago
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆28Updated last year
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆26Updated last year
• PacificBiosciences / pbipa
  Improved Phased Assembler
  ☆28Updated 3 years ago
• BrendelGroup / AEGeAn
  Integrated toolkit for analysis and evaluation of annotated genomes
  ☆25Updated 5 months ago
• compbiol / CAMSA
  CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies
  ☆24Updated 5 years ago