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
• kcleal / pywfa
  Python wrapper for wavefront alignment using WFA2-lib
  ☆35Updated 10 months ago
• rcedgar / urmap
  URMAP ultra-fast read mapper
  ☆38Updated 5 years ago
• jts / bri
  Bam Read Index - Extract alignments from a bam file by readname
  ☆27Updated last year
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆29Updated 9 months ago
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆48Updated 4 years ago
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated 3 months ago
• lh3 / gffio
  ☆32Updated 2 years ago
• alshai / levioSAM
  Lift-over alignments from variant-aware references
  ☆34Updated 2 years ago
• jltsiren / gbwtgraph
  GBWT-based handle graph
  ☆31Updated 2 months ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• natir / fpa
  Filter of Pairwise Alignement
  ☆44Updated 3 years ago
• shenwei356 / wfa
  Wavefront alignment algorithm (WFA) in Golang
  ☆32Updated last month
• pierrepeterlongo / back_to_sequences
  ☆45Updated last month
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• Parsoa / SVDSS
  Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
  ☆45Updated 2 weeks ago
• richarddurbin / syng
  syncmer graphs, and perhaps other sorts of sequence graphs
  ☆21Updated 5 months ago
• nanoporetech / minimappy
  Python bindings to minimap2
  ☆16Updated 8 years ago
• mikolmogorov / pbclip
  A simple tool to fix PacBio fasta/q that was not properly split into subreads
  ☆15Updated 4 years ago
• kcleal / svbench
  Benchmark structural variant calls against a reference set
  ☆17Updated 10 months ago
• tobiasrausch / lorax
  A long-read analysis toolbox for cancer and population genomics
  ☆23Updated 2 months ago
• zhixingfeng / iGDA
  Detect and phase minor SNVs from long-read sequencing data
  ☆13Updated 3 years ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆36Updated last year
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated 5 months ago
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆45Updated last month
• benedictpaten / marginPhase
  ☆34Updated 5 years ago
• jts / smrest
  Tumour-only somatic mutation calling using long reads
  ☆27Updated 10 months ago
• fritzsedlazeck / SVCollector
  Method to optimally select samples for validation and resequencing
  ☆28Updated 4 years ago
• marbl / T2T-Browser
  Genome browser hub for the T2T genomes and resources
  ☆23Updated last week
• HongzheGuo / deBGA
  de Bruijn Graph-based read aligner
  ☆33Updated 7 years ago