ArticleScientific reports2019
Featherweight long read alignment using partitioned reference indexes.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Context-aware simulation enables systematic optimization of long-read mapping parameters.GigaScience · 2026Article
- Taming large-scale genomic analyses via sparsified genomics.Nature communications · 2025Article
- Long-Read MDM4 Sequencing Reveals Aberrant Isoform Landscape in Metastatic Melanomas.International journal of molecular sciences · 2024Article
- Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining.Scientific reports · 2023Article
- Resolving complex structural variants via nanopore sequencing.Frontiers in genetics · 2023Review
- Article
- Bioinformatic Challenges Detecting Genetic Variation in Precision Medicine Programs.Frontiers in medicine · 2022Review
- LazyB: fast and cheap genome assembly.Algorithms for molecular biology : AMB · 2021Article
- A Round Trip to the Desert:Frontiers in microbiology · 2021Article
- Portable nanopore analytics: are we there yet?Bioinformatics (Oxford, England) · 2020Article
- GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis.BMC bioinformatics · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent of Nanopore sequencing has realised portable genomic research and applications. However, state of the art long read aligners and large reference genomes are not compatible with most mobile computing devices due to their high memory requirements. We show how memory requirements can be reduced through parameter optimisation and reference genome partitioning, but highlight the associated limitations and caveats of these approaches. We then demonstrate how these issues can be overcome through an appropriate merging technique. We incorporated multi-index merging into the Minimap2 aligner and demonstrate that long read alignment to the human genome can be performed on a system with 2 GB RAM with negligible impact on accuracy.
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Registered trials
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