RECOMB-Seq 2022 Proceedings

San Diego, CA, United States, May 20 - 21, 2022.

PC Chair: Ben Langmead, Johns Hopkins University.
Keynote Speakers: Arang Rhie and Siavash Mirarab.

Full Papers

  • Sequence-based pangenomic core detection. Tizian Schulz, Roland Wittler and Jens Stoye. iScience, 25 (6): 104413, (2022)
  • scTagger: Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments. Ghazal Ebrahimi, Baraa Orabi, Meghan Robinson, Cedric Chauve, Ryan Flannigan and Faraz Hach. iScience, 25 (7): 104530, (2022)
  • Genetic polyploid phasing from low-depth progeny samples. Sven Schrinner, Rebecca Serra Mari, Richard Finkers, Paul Arens, Björn Usadel, Tobias Marschall and Gunnar W. Klau. iScience, 25 (6): 104461, (2022)
  • BOA: a partitioned view of genome assembly . Priyanka Ghosh, Xiaojing An, Patrick Keppler, Sureyya Emre Kurt, Umit Catalyurek, Sriram Krishnamoorthy, Ponnuswamy Sadayappan, Aravind Sukumaran Rajam and Ananth Kalyanaraman. iScience, 25 (11): 105273, (2022)
  • Mapping-friendly sequence reductions: going beyond homopolymer compression. Luc Blassel, Paul Medvedev and Rayan Chikhi. iScience, 25 (11): 105305, (2022)
  • BinSPreader: refine binning results for fuller MAG reconstruction . Ivan Tolstoganov, Yury Kamenev, Roman Kruglikov, Sofia Ochkalova and Anton Korobeynikov. iScience, 25 (8): 104770, (2022)
  • Flexible seed size enables ultra-fast and accurate read alignment. Kristoffer Sahlin. overlay preprint
  • Sparse and skew hashing of k-mers. Giulio Ermanno Pibiri. overlay preprint
  • Metagenome assembly of high-fidelity long reads with hifiasm-meta. Xiaowen Feng, Haoyu Cheng, Daniel Portik and Heng Li. overlay preprint
  • Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees. Camille Marchet and Antoine Limasset. overlay preprint
  • Improved structural variant discovery in hard-to-call regions using sample-specific string detection from accurate long reads. Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari and Rayan Chikhi. overlay preprint
  • The minimizer Jaccard estimator is biased and inconsistent. Mahdi Belbasi, Antonio Blanca, Robert S. Harris, David Koslicki and Paul Medvedev. overlay preprint

Short Talks Selected from Abstracts

  • A trans-ancestry genomics-based approach to study the interplay between the the immune system, pathogen virulence, and HLA type, ancestry, and sepsis outcome. Serghei Mangul.
  • Genotyping short tandem repeats using long reads. Helyaneh Ziaei Jam and Melissa Gymrek.
  • Metabuli: a metagenomic classifier that combines protein- and DNA-level classification to achieve both high sensitivity and specificity. Jaebeom Kim and Martin Steinegger.
  • Rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing. Kerui Peng and Serghei Mangul.
  • Detection of somatic mosaicism at short tandem repeats from NGS data. Aarushi Sehgal and Melissa Gymrek.

Posters

  • Finding Significant Genes and Pathways Across Viruses in CRISPR-Cas9 Screen Database. Elianna Kondylis, Jacklyn Luu, Kyle Awayan, Andreas Puschnik, Angela Pisco.
  • Metabuli: a metagenomic classifier that combines protein- and DNA-level classification to achieve both high sensitivity and specificity. Jaebeom Kim and Martin Steinegger.
  • Sketching and sampling approaches for fast and accurate long read classification. Arun Das and Michael Schatz.
  • Theory of local k-mer selection with applications to long-read alignment. Jim Shaw and Yun William Yu.
  • Metagenome assembly of high-fidelity long reads with hifiasm-meta. Xiaowen Feng, Haoyu Cheng, Daniel Portik and Heng Li.
  • Automated telomere-to-telomere genome assembly with PacBio HiFi and ultra-long ONT data. Mikko Rautiainen, Sergey Nurk, Brian Walenz, Adam M Phillippy, Sergey Koren.
  • Unlocking the microblogging potential for science and medicine. Karishma Chhugani and Serghei Mangul.