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Annual Review of Genomics and Human Genetics|May 5, 2015
Alignment of Next-Generation Sequencing ReadsKnut Reinert, Ben Langmead, David Weese, et al.Genome Biology|March 6, 2009
Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeBen Langmead, Cole Trapnell, Mihai Pop, et al.Bioinformatics (Oxford, England)|April 23, 2020
Vargas: heuristic-free alignment for assessing linear and graph read alignersCharlotte A Darby, Ravi Gaddipati, Michael C Schatz, et al.Biorxiv : the Preprint Server for Biology|September 25, 2023
Measuring, visualizing and diagnosing reference bias with biastoolsMao-Jan Lin, Sheila Iyer, Nae-Chyun Chen, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|January 18, 2022
MONI: A Pangenomic Index for Finding Maximal Exact MatchesMassimiliano Rossi, Marco Oliva, Ben Langmead, et al.Genome Biology|April 19, 2024
Measuring, visualizing, and diagnosing reference bias with biastoolsMao-Jan Lin, Sheila Iyer, Nae-Chyun Chen, et al.Nucleic Acids Research|August 9, 2019
Analyzing whole genome bisulfite sequencing data from highly divergent genotypesPhillip Wulfridge, Ben Langmead, Andrew P Feinberg, et al.Genome Biology|January 5, 2021
Reference flow: reducing reference bias using multiple population genomesNae-Chyun Chen, Brad Solomon, Taher Mun, et al.Iscience|January 7, 2026
Run-length compressed metagenomic read classification with SMEM-finding and taggingLore Depuydt, Omar Y Ahmed, Jan Fostier, et al.Genome Biology|May 18, 2023
SPUMONI 2: improved classification using a pangenome index of minimizer digestsOmar Y Ahmed, Massimiliano Rossi, Travis Gagie, et al.Pageof 13