Sequence analysis (methods)

In this topical collection (520 articles)

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1. Methodology article

   A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy

   Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers… Article:586

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2. Research Article

   HISEA: HIerarchical SEed Aligner for PacBio data

   Nilesh Khiste, Lucian Ilie Article:564

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3. Methodology Article

   An Eigenvalue test for spatial principal component analysis

   V. Montano, T. Jombart Article:562

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4. Software

   acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

   Markus Lux, Jan Krüger, Christian Rinke, Irena Maus, Andreas Schlüter… Article:543

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5. Research Article

   Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach

   Oyetunji E. Ogundijo, Xiaodong Wang Article:541

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6. Methodology article

   MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

   Jingting Xu, Shimeng Liu, Ping Yin, Serdar Bulun, Yang Dai Article:540

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7. Methodology Article

   CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

   Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol… Article:538

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8. Research article

   Towards practical privacy-preserving genome-wide association study

   Charlotte Bonte, Eleftheria Makri, Amin Ardeshirdavani, Jaak Simm… Article:537

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9. Methodology article

   NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors

   John M. Gaspar Article:536

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10. Methodology Article

    Decontaminating eukaryotic genome assemblies with machine learning

    Janna L. Fierst, Duncan A. Murdock Article:533

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11. Software

    GLUE: a flexible software system for virus sequence data

    Joshua B. Singer, Emma C. Thomson, John McLauchlan, Joseph Hughes… Article:532

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12. Research Article

    New tools to analyze overlapping coding regions

    Amir H. Bayegan, Juan Antonio Garcia-Martin, Peter Clote Article:530

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13. Software

    DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data

    John M. Gaspar, Ronald P. Hart Article:528

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14. Methodology Article

    An efficient error correction algorithm using FM-index

    Yao-Ting Huang, Yu-Wen Huang Article:524

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15. Research article

    Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations

    Camilo Andrés Mora Osorio, Andrés Fernando González Barrios Article:522

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16. Research Article

    HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data

    Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo… Article:516

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17. Research Article

    Fast batch searching for protein homology based on compression and clustering

    Hongwei Ge, Liang Sun, Jinghong Yu Article:508

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18. Methodology Article

    Swellix: a computational tool to explore RNA conformational space

    Nathan Sloat, Jui-Wen Liu, Susan J. Schroeder Article:504

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19. Research article

    Predicting the recurrence of noncoding regulatory mutations in cancer

    Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung, Jung Kyoon Choi Article:492

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20. Methodology Article

    Reconstructing cancer karyotypes from short read data: the half empty and half full glass

    Rami Eitan, Ron Shamir Article:488

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