CMU-SAFARI / FastRemapLinks
FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: https://arxiv.org/pdf/2201.06255.pdf
☆26Updated 3 years ago
Alternatives and similar repositories for FastRemap
Users that are interested in FastRemap are comparing it to the libraries listed below
Sorting:
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Updated last year
- De-novo Assembly Structural Variant Caller☆13Updated 9 years ago
- Kmer based genotyper for short reads.☆23Updated 4 years ago
- This is the Haplotypo repository☆22Updated last year
- Phase reads, assemble haplotypes and detect SVs☆19Updated 5 years ago
- MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes☆30Updated 5 years ago
- Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.☆29Updated 7 years ago
- A tool set to assess the quality of the per read phasing and reduce the errors.☆13Updated 5 years ago
- Functions to compare a SV call sets against a truth set.☆30Updated 7 months ago
- Benchmark structural variant calls against a reference set☆18Updated 2 weeks ago
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆28Updated last year
- ☆14Updated 2 years ago
- ☆15Updated last year
- The Vertebrate Genomes Project Mitogenome Assembly Pipeline☆19Updated 2 years ago
- Genotyping of segregating mobile elements insertions☆19Updated 4 years ago
- ☆16Updated 4 years ago
- Gene copy number prediction from k-mer frequencies☆14Updated last year
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Updated 2 months ago
- ☆16Updated 8 years ago
- A module for improving the insertion sequences of structural variant calls☆33Updated 4 years ago
- A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.☆18Updated 3 weeks ago
- Detect and phase minor SNVs from long-read sequencing data☆14Updated 4 years ago
- Tools for merging Tandem Repeat VCF files☆37Updated 9 months ago
- Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data☆16Updated last year
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆29Updated last year
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆25Updated 5 years ago
- Benchmarking variant calling in polyploids☆15Updated 4 years ago
- Long-read aligner to pangenome graphs☆29Updated last year
- A tool for recovering synteny blocks from multiple alignment☆32Updated 4 years ago
- Improved Phased Assembler☆28Updated 3 years ago