Alternatives and similar repositories for chain2paf

Users that are interested in chain2paf are comparing it to the libraries listed below

• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆15Updated 2 months ago
• ekg / pafplot
  base-level dotplots from PAF alignments
  ☆27Updated last month
• Gaius-Augustus / clamsa
  ClaMSA (Classify Multiple Sequence Alignments).
  ☆13Updated 11 months ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆25Updated 11 months ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆26Updated last week
• richarddurbin / syng
  syncmer graphs, and perhaps other sorts of sequence graphs
  ☆21Updated 7 months ago
• pierrepeterlongo / kmer2sequences
  Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
  ☆21Updated 2 years ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated last year
• ldenti / palss
  ☆22Updated last month
• marbl / T2T-Browser
  Genome browser hub for the T2T genomes and resources
  ☆24Updated last month
• Walfred-MA / Ctyper
  Genotyping of copy number sensitive allele-specific haplotypes
  ☆23Updated this week
• lrobidou / KFC
  ☆19Updated 8 months ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 4 years ago
• GP2code / CNV-Finder
  Expedite large-scale identification of CNVs within predefined genomic regions. Online app available for those with GP2 Tier 2 Access.
  ☆11Updated 4 months ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆29Updated this week
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated last year
• edawson / svaha2
  Linear-time, low-memory construction of variation graphs
  ☆20Updated 5 years ago
• chfi / pafview
  ☆17Updated 9 months ago
• ban-m / jtk
  JTK -- a regional diploid genome assembler
  ☆25Updated last year
• tobiasrausch / lorax
  A long-read analysis toolbox for cancer and population genomics
  ☆23Updated 4 months ago
• zhixingfeng / iGDA
  Detect and phase minor SNVs from long-read sequencing data
  ☆14Updated 3 years ago
• mbhall88 / skc
  Shared k-mer content between two genomes
  ☆18Updated 2 years ago
• collaborativebioinformatics / GeneVar
  ☆12Updated 4 years ago
• mbhall88 / pafpy
  A lightweight library for working with PAF (Pairwise mApping Format) files
  ☆30Updated 3 years ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆26Updated last year
• fulcrumgenomics / fgsv
  Tools to gather evidence for structural variation via breakpoint detection.
  ☆19Updated 6 months ago
• luntergroup / polyploid
  Benchmarking variant calling in polyploids
  ☆15Updated 3 years ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• jltsiren / gbwtgraph
  GBWT-based handle graph
  ☆31Updated last week
• ComparativeGenomicsToolkit / taffy
  This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
  ☆29Updated 2 months ago