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New strategies to improve minimap2 alignment accuracy
[article]
2021
arXiv
pre-print
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Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. ...
Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions up to 100kb by default, addressing major weakness in minimap2 v2.18 or earlier ...
ACKNOWLEDGEMENTS We thank Arang Rhie and Chirag Jain for providing motivating examples for which older minimap2 underperforms. Funding: This work is funded by NHGRI grant R01HG010040. ...
arXiv:2108.03515v1
fatcat:dlheomzaxrhinlioqalffyr4xa
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment
[article]
2021
bioRxiv
pre-print
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These improvements, in turn, lead to improved accuracy for structural variant calling performance on human genome datasets compared to either of the read mapping methods alone. ...
Various heuristics and scoring schemas have been implemented in widely-used read mappers (minimap2 and NGMLR) to optimize for speed or accuracy, which have variable performance across different genomic ...
Acknowledgments The authors want to thank Dreycey Albin for contributing critical discussion. ...
doi:10.1101/2021.05.29.446291
fatcat:52u6tscdunelhddikottl5vlvu
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment
2021
GigaScience
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These improvements, in turn, lead to improved accuracy for structural variant calling performance on human genome datasets compared to either of the read-mapping methods alone. ...
Various heuristics and scoring schemas have been implemented in widely used read mappers (minimap2 and NGMLR) to optimize for speed or accuracy, which have variable performance across different genomic ...
Improved SV calling based on Vulcan's results can be attributed to leveraging the strengths of the long-read alignment strategies found in minimap2 and NGMLR. ...
doi:10.1093/gigascience/giab063
pmid:34561697
pmcid:PMC8463296
fatcat:ifdxijwk5jdvhcry5syzv46syq
Faster short-read mapping with strobemer seeds in syncmer space
[article]
2021
bioRxiv
pre-print
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Our protocol allows us to create longer seeds while preserving mapping accuracy. A longer seed length reduces the number of candidate regions which allows faster mapping and alignment. ...
seeding-and-chaining strategy. ...
We implemented our strategy in a proof-of-concept aligner and mapping tool strobealign 3-4x faster than state-of-the-art aligner minimap2 while having roughly the same accuracy. strobealign demonstrates ...
doi:10.1101/2021.06.18.449070
fatcat:p6tb3t4nhreg3gzfdtd6vhwgtu
Pan-genomic Matching Statistics for Targeted Nanopore Sequencing
[article]
2021
bioRxiv
pre-print
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When used to target a specific strain in a mock community, SPUMONI has similar accuracy as minimap2 when both are run against an index containing many strains per species. ...
However SPUMONI is 12 times faster than minimap2. SPUMONI's index and peak memory footprint are also 15 to 4 times smaller than minimap2, respectively. ...
As nanopore sequencing continues to improve, both base-calling accuracy and per-instruction throughput will likely improve. ...
doi:10.1101/2021.03.23.436610
fatcat:bjwrzvkbhvbqtpnhxbnujv45j4
Featherweight long read alignment using partitioned reference indexes
[article]
2018
bioRxiv
pre-print
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We extend the Minimap2 aligner and demonstrate that long read alignment to the human genome can be performed on a system with 2GB RAM with negligible impact on accuracy. ...
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. ...
Acknowledgements We thank Heng Li, the author of Minimap2 for assisting us in understanding the code, providing us with valuable insights and suggestions through Github issues, and integrating our method ...
doi:10.1101/386847
fatcat:r7aowocki5glvlc2d2jhep7g6y
Accel-Align: A Fast Sequence Mapper and Aligner based on the Seed-Embed-Extend Method
[article]
2020
bioRxiv
pre-print
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Motivation: Improvements in sequencing technology continue to drive sequencing cost towards 100$ per genome. ...
Results: Motivated by algorithmic advances in randomized low-distortion embeddings, we introduce seed-embed-extend (SEE), a new design methodology for developing sequence mappers and aligners. ...
Conclusions As sequencing technologies continue to increase read length while improving throughput and accuracy, we believe that randomized embeddings open up new avenues for optimization that cannot be ...
doi:10.1101/2020.07.20.211888
fatcat:6j7ed6lrkneljc4wn3l2mypks4
Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method
2021
BMC Bioinformatics
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As sequencing technologies continue to increase read length while improving throughput and accuracy, we believe that randomized embeddings open up new avenues for optimization that cannot be achieved by ...
Improvements in sequencing technology continue to drive sequencing cost towards $100 per genome. ...
Conclusions As sequencing technologies continue to increase read length while improving throughput and accuracy, we believe that randomized embeddings open up new avenues for optimization that cannot be ...
doi:10.1186/s12859-021-04162-z
pmid:34016035
fatcat:3zpke4xusjh7jclklsajmlnmci
Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications
2020
Nucleic Acids Research
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We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. ...
Across multiple whole-genome long-read datasets, DuploMap aligned an additional 8–21% of the reads in segmental duplications with high confidence relative to Minimap2. ...
Miga et al. (25) have used a unique k-mer-based mapping strategy to improve read mapping to generate baselevel DNA methylation maps for the centromere of the X chromosome. ...
doi:10.1093/nar/gkaa829
pmid:33035301
fatcat:26vgfumbbbfdvlgkkrksigf2ie
Minimap2: pairwise alignment for nucleotide sequences
2018
Bioinformatics
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Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions (INDELs) and introduces new heuristics to reduce spurious alignments. ...
Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. ...
We are also grateful to minimap2 users who have greatly helped to suggest features and to fix various issues. ...
doi:10.1093/bioinformatics/bty191
pmid:29750242
fatcat:c3lhwod4mvglnc4kqrkvsv6kxe
IMOS: improved Meta-aligner and Minimap2 On Spark
2019
BMC Bioinformatics
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In its single-node mode, IMOS is an Improved version of Meta-aligner (IM) enhancing both its accuracy and speed. IM is up to 6x faster than the original Meta-aligner. ...
Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed. ...
Acknowledgements The authors would like to cordially thank Damoun Nashta'ali and Mohammad Javad Rezae Seraji for their helpful advices. ...
doi:10.1186/s12859-018-2592-5
fatcat:qkpapwj7vzhbdmg6djttldbc5i
Sensitive alignment using paralogous sequence variants improves long read mapping and variant calling in segmental duplications
[article]
2020
bioRxiv
pre-print
Preserved Fulltext
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We describe a probabilistic method, DuploMap, designed to improve the accuracy of long read mapping in segmental duplications. ...
On simulated datasets, Duplomap increased the percentage of correctly mapped reads with high confidence for multiple long-read aligners including Minimap2 (74.3% to 90.6%) and BLASR (82.9% to 90.7%) while ...
[25] have used a unique k-mer based mapping strategy to improve read mapping to generate base-level DNA methylation maps for the centromere of the X chromosome. ...
doi:10.1101/2020.07.15.202929
fatcat:jqcwvac62jfpbha3pgtzhazdie
A long read mapping method for highly repetitive reference sequences
[article]
2020
bioRxiv
pre-print
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variants within near-identical repeats compared to minimap2 (39.62%, 5.88%) and NGMLR (56.60%, 36.11%) respectively. ...
To address the above problem, we propose a novel, long read mapping method that addresses allelic bias by making use of minimal confidently alignable substrings (MCASs). ...
We also acknowledge Heng Li for responding to our queries regarding minimap2 code. Winnowmap2 and Winnowmap were developed on top of minimap2 code. ...
doi:10.1101/2020.11.01.363887
fatcat:eq5il5khhzfdphfb7zylffnknu
Accurate spliced alignment of long RNA sequencing reads
2021
Bioinformatics
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While uLTRA obtains its accuracy using annotations, it can also be used as a wrapper around minimap2 to align reads outside annotated regions. ...
However, the error rate and sequencing length of the reads create new challenges for accurately aligning them, particularly around small exons. ...
Acknowledgements We would like to thank Paul Medvedev for helpful feedback and comments. ...
doi:10.1093/bioinformatics/btab540
pmid:34302453
pmcid:PMC8665758
fatcat:v75pt7c3kzcttlgxh6etckoe6e
Evaluating Structural Variation Detection Tools for Long-Read Sequencing Datasets in Saccharomyces cerevisiae
2020
Frontiers in Genetics
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Therefore, we developed an analysis workflow that combined two alignment tools (NGMLR and minimap2) and five callers (Sniffles, Picky, smartie-sv, PBHoney, and NanoSV) to evaluate the SV detection in six ...
The accuracy of SV regions was validated by re-aligning raw reads in diverse alignment tools, SV callers, experimental conditions, and sequencing platforms. ...
Although we had proposed the strategy to validate SVs by using re-alignment of raw long read for the different callers, the integration and improvement of the results from the different callers need further ...
doi:10.3389/fgene.2020.00159
pmid:32211024
pmcid:PMC7075250
fatcat:pvtefjzr5ra4zgxvcvymhzqxcm
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