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New strategies to improve minimap2 alignment accuracy [article]

Heng Li
2021 arXiv   pre-print
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]

Yilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, Fritz J Sedlazeck, Todd J Treangen
2021 bioRxiv   pre-print
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

Yilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, Fritz J Sedlazeck, Todd J Treangen
2021 GigaScience  
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]

Kristoffer Sahlin
2021 bioRxiv   pre-print
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]

Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael Schatz, Travis Gagie, Christina Boucher, Ben Langmead
2021 bioRxiv   pre-print
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]

Hasindu Gamaarachchi, Sri Parameswaran, Martin Smith
2018 bioRxiv   pre-print
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]

Yiqing Yan, Nimisha Chaturvedi, Raja Appuswamy
2020 bioRxiv   pre-print
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

Yiqing Yan, Nimisha Chaturvedi, Raja Appuswamy
2021 BMC Bioinformatics  
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

Timofey Prodanov, Vikas Bansal
2020 Nucleic Acids Research  
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

Heng Li, Inanc Birol
2018 Bioinformatics  
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

Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi, Seyed Abolfazl Motahari
2019 BMC Bioinformatics  
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]

Timofey Prodanov, Vikas Bansal
2020 bioRxiv   pre-print
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]

Chirag Jain, Arang Rhie, Nancy Hansen, Sergey Koren, Adam M. Phillippy
2020 bioRxiv   pre-print
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

Kristoffer Sahlin, Veli Mäkinen, Peter Robinson
2021 Bioinformatics  
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

Mei-Wei Luan, Xiao-Ming Zhang, Zi-Bin Zhu, Ying Chen, Shang-Qian Xie
2020 Frontiers in Genetics  
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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