alshai / levioSAM
Lift-over alignments from variant-aware references
☆34Updated 2 years ago
Alternatives and similar repositories for levioSAM:
Users that are interested in levioSAM are comparing it to the libraries listed below
- ☆28Updated 3 weeks ago
- run-length BWT tools for genomic sequences☆19Updated 2 years ago
- MONI: A Pangenomic Index for Finding MEMs☆37Updated last month
- URMAP ultra-fast read mapper☆38Updated 4 years ago
- Population-wide Deletion Calling☆35Updated 2 weeks ago
- Identification of segmental duplications in the genome☆27Updated 3 years ago
- Layout module for raw de novo genome assembly of long uncorrected reads.☆21Updated 4 years ago
- ☆16Updated 7 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆54Updated 2 years ago
- convert a multi-sample VCF file to a multiple sequence alignment (C)☆13Updated 6 years ago
- Comprehensive alignment, whole-genome coverage, and capture coverage statistics.☆19Updated 4 months ago
- This repo is deprecated. Please use gfatools instead.☆16Updated 6 years ago
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆29Updated 7 months ago
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆24Updated 5 years ago
- Exact Tandem Repeat Finder (not a TRF replacement)☆49Updated 5 years ago
- extract MSAs from genome variation graphs☆33Updated 4 years ago
- recompute GFA link overlaps☆25Updated 2 years 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
- Method to optimally select samples for validation and resequencing☆27Updated 4 years ago
- GFA insert into GenomicSQLite☆49Updated 3 years ago
- Minimizer-based assembly scaffolding and mapping using long reads☆39Updated 6 months ago
- An algorithm for centromere assembly using long error-prone reads☆26Updated 3 years ago
- A streaming method for mapping nanopore raw signals☆32Updated 3 years ago
- base-accurate DNA sequence alignments using edlib and mashmap2☆33Updated 4 years ago
- ☆34Updated 5 years ago
- Assembler for raw de novo genome assembly of long uncorrected reads.☆37Updated 5 years ago
- Indel-aware consensus for aligned BAM☆21Updated last month
- genotyping by Mapping-free ALternate-allele detection of known VAriants☆10Updated 2 years ago
- Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.☆22Updated 6 years ago