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 2 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☆24Updated last year
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆27Updated 9 months ago
- Phase reads, assemble haplotypes and detect SVs☆19Updated 4 years ago
- Kmer based genotyper for short reads.☆23Updated 3 years ago
- ☆14Updated last year
- This is the Haplotypo repository☆20Updated last year
- Functions to compare a SV call sets against a truth set.☆30Updated 3 weeks ago
- ☆32Updated 2 years ago
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆27Updated last year
- Identification of segmental duplications in the genome☆27Updated 3 years ago
- A module for improving the insertion sequences of structural variant calls☆30Updated 4 years ago
- Benchmark structural variant calls against a reference set☆17Updated 8 months ago
- Gene copy number prediction from k-mer frequencies☆13Updated 11 months ago
- use variant nesting information to flter overlapping sites from vg deconstruct output☆26Updated last month
- Fast in-silico normalization algorithm for NGS data☆23Updated 3 years ago
- easy_sbatch - Batch submitting Slurm jobs with script templates☆17Updated 3 years ago
- MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes☆30Updated 4 years ago
- Population-wide Deletion Calling☆35Updated 3 months ago
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆23Updated last year
- Tool for decomposition centromeric assemblies and long reads into monomers☆36Updated 2 years ago
- De-novo Assembly Structural Variant Caller☆13Updated 8 years ago
- Convert HAL to VG☆22Updated 11 months ago
- URMAP ultra-fast read mapper☆39Updated 5 years ago
- Phasing reads with secondary alignments☆19Updated 7 months ago
- Structural variant (SV) analysis tools☆36Updated last year
- 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
- CNEFinder: Finding Conserved Non-coding Elements in Genomes☆24Updated 3 years ago
- Method to optimally select samples for validation and resequencing☆28Updated 4 years ago
- Benchmarking variant calling in polyploids☆15Updated 3 years ago
- Exact Tandem Repeat Finder (not a TRF replacement)☆49Updated 5 years ago