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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...-quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing step that uses reads aligned to the draft assembly to identify necessary edits. However, current methods struggle to find a balance between over- and underpolishing...
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Methods: MAVID: Constrained Ancestral Alignment of Multiple Sequences
- Nicolas Bray and
- Lior Pachter
Genome Res. April 2004 14: 693-699; doi:10.1101/gr.1960404
...). After the ancestral sequence calculation, su and sv are aligned with AVID ( Bray et al. 2003 ). AVID is a hierarchical global pairwise alignment program that iteratively anchors maximal exact matches and wobble matches (i.e., matches which are exact, except for possible mismatches every third base...
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Methods: Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- Benedict Paten,
- Javier Herrero,
- Kathryn Beal,
- Stephen Fitzgerald,
- and Ewan Birney
Genome Res. November 2008 18: 1814-1828; Published in Advance October 10, 2008, doi:10.1101/gr.076554.108
...et al. 2003a ) uses a k -mer (each k -mer is an ungapped local alignment of length k ) chaining procedure to find initial local alignments around which a global alignment is constructed. Mavid ( Bray and Pachter 2004 ) recursively defines a global alignment using maximally nonrepetitive ungapped...
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Methods: Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
- Aaron C.E. Darling,
- Bob Mau,
- Frederick R. Blattner,
- and Nicole T. Perna
Genome Res. July 2004 14: 1394-1403; doi:10.1101/gr.2289704
...and horizontal transfer. Our methods have been implemented in a software package called Mauve. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. We have evaluated the quality of Mauve alignments and drawn comparison to other...
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METHODS: LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
- Michael Brudno,
- Chuong B. Do,
- Gregory M. Cooper,
- Michael F. Kim,
- Eugene Davydov,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- Arend Sidow,
- and Serafim Batzoglou
Genome Res. April 1, 2003 13: 721-731; Published in Advance March 12, 2003, doi:10.1101/gr.926603
...lengths. Efficient global aligners such as MUMmer ( Delcher et al. 1999 , 2002 ), GLASS ( Batzoglou et al. 2000 ), and AVID ( Bray et al. 2003 ) rely on anchoring . First, they detect local similarities between the two sequences. Second, they select and fix an ordered set of local similarities...
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Chicken Special/Resources: Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
- Ivan Ovcharenko,
- Gabriela G. Loots,
- Belinda M. Giardine,
- Minmei Hou,
- Jian Ma,
- Ross C. Hardison,
- Lisa Stubbs,
- and Webb Miller
Genome Res. January 2005 15: 184-194; Published in Advance December 8, 2004, doi:10.1101/gr.3007205
...alignments with a selected reference sequence ( Mayor et al. 2000 ; Schwartz et al. 2000 ; Ovcharenko et al. 2004b ) or as a full multiple-sequence global or pseudoglobal alignment ( Thompson et al. 1994 ; Bray et al. 2003 ; Brudno et al. 2003 ; Schwartz et al. 2003a ; Ovcharenko et al. 2004a ). Applications...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
..., Amathus Therapeutics, Aligning Science Across Parkinson's (ASAP), Avid Radiopharmaceuticals, Bial Biotech, Biogen, BioLegend, BlueRock Therapeutics, Bristol Myers Squibb, Calico Life Sciences LLC, Celgene Corporation, DaCapo Brainscience, Denali Therapeutics, The Edmond J. Safra Foundation, Eli Lilly...
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METHODS: SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model
- Marina Alexandersson,
- Simon Cawley,
- and Lior Pachter
Genome Res. March 1, 2003 13: 496-502; Published in Advance February 12, 2003, doi:10.1101/gr.424203
...the two input sequences using the AVID global alignment tool ( Bray et al. 2003 ). AVID is a recursive anchor-based alignment algorithm that generalizes and extends GLASS ( Pachter 1999 ; Batzoglou et al. 2000 ) and MUMmer ( Delcher et al. 1999 ). The AVID global alignment was “relaxed” in two steps...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...are essential for detecting TFs below 3%. NanoRCS provides an opportunity for cost-effective and rapid sample processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.A recent advancement in cancer...
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RESOURCE: CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting
- Eugene Berezikov,
- Victor Guryev,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. January 2004 14: 170-178; Published in Advance December 12, 2003, doi:10.1101/gr.1642804
...of the performance of CONREAL with the global alignment programs LAGAN and AVID using a reference data set, shows that CONREAL performs equally well for closely related species like rodents and human, and has a clear added value for aligning promoter elements of more divergent species like human and fish...

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