NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids bias…
☆88May 15, 2019Updated 6 years ago
Alternatives and similar repositories for NextGenMap
Users that are interested in NextGenMap are comparing it to the libraries listed below
Sorting:
- A software for discovery, genotyping and characterization of structural variants☆22Sep 11, 2024Updated last year
- Toolkit for extracting SVs from long sequences and benchmarking variant callers☆13Jan 10, 2017Updated 9 years ago
- RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes☆18Apr 2, 2020Updated 5 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Linear-time, low-memory construction of variation graphs☆20Feb 3, 2020Updated 6 years ago
- De novo genome assembly and multisample variant calling☆112Mar 28, 2019Updated 6 years ago
- Integrated Variant Caller☆17Mar 15, 2018Updated 8 years ago
- ☆13Jan 23, 2020Updated 6 years ago
- A tool to benchmark mappers and different parameters within minutes☆44Jul 2, 2019Updated 6 years ago
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 4 years ago
- reference free variant assembly☆34Jul 14, 2023Updated 2 years ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated 11 months ago
- A method for variant graph genotyping based on exact alignment of k-mers☆87Apr 1, 2019Updated 6 years ago
- Copy number estimation of highly duplicated sequences☆10Aug 15, 2017Updated 8 years ago
- Analysis tool for Nanopore sequencing data☆34Apr 15, 2019Updated 6 years ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆225Sep 18, 2025Updated 6 months ago
- Efficient phylogenomic software by maximum likelihood☆204Nov 4, 2021Updated 4 years ago
- Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities☆25Oct 31, 2019Updated 6 years ago
- NovoGraph: building whole genome graphs from long-read-based de novo assemblies☆46Feb 23, 2021Updated 5 years ago
- The Modular Aligner and The Modular SV Caller☆46Jul 18, 2023Updated 2 years ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆399Aug 30, 2025Updated 6 months ago
- Recommended Graphtyper pipelines☆15Feb 22, 2021Updated 5 years ago
- Online material and code base for the article Coordinates and Intervals in Graph Based Reference Genomes☆11May 2, 2017Updated 8 years ago
- don't get DUP'ed or DEL'ed by your putative SVs.☆107Dec 14, 2020Updated 5 years ago
- Population Reference Graphs for the HLA and MHC.☆35Dec 18, 2018Updated 7 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated last year
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆54Mar 7, 2025Updated last year
- Error correction and variant calling algorithm for nanopore sequencing☆26Apr 23, 2016Updated 9 years ago
- C++ htslib/bwa-mem/fermi interface for interrogating sequence data☆138Sep 16, 2025Updated 6 months ago
- Long Approximate Matches-based Split Aligner☆13Apr 6, 2017Updated 8 years ago
- RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.☆14Nov 10, 2025Updated 4 months ago
- Compressive Read-mapping Accelerator☆14Sep 7, 2016Updated 9 years ago
- AlignerBoost is a generalized software toolkit for boosting Next-Gen sequencing mapping precision using a Bayesian based mapping quality …☆11Mar 1, 2022Updated 4 years ago
- IndexTools is a toolkit for extremely fast NGS analysis based on index files.☆17Aug 19, 2022Updated 3 years ago
- Population-scale detection of novel sequence insertions☆27Aug 16, 2022Updated 3 years ago
- de Bruijn Graph REAd mapping Tool☆14Jul 12, 2017Updated 8 years ago
- ☆12Jan 21, 2016Updated 10 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Pan-Genomic Matching Statistics☆55Apr 3, 2024Updated last year