HISAT: a fast spliced aligner with low memory requirements
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TLDR
Tests showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method, and requires only 4.3 gigabytes of memory.Abstract:
HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT's hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ∼64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.read more
Citations
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Journal ArticleDOI
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
TL;DR: This work presents a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index, and uses it to represent and search an expanded model of the human reference genome.
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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
TL;DR: This protocol describes all the steps necessary to process a large set of raw sequencing reads and create lists of gene transcripts, expression levels, and differentially expressed genes and transcripts.
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Shifting the limits in wheat research and breeding using a fully annotated reference genome
Rudi Appels,Rudi Appels,Kellye Eversole,Nils Stein,Nils Stein,Catherine Feuillet,Beat Keller,Jane Rogers,Curtis J. Pozniak,Frédéric Choulet,Assaf Distelfeld,Jesse Poland,Gil Ronen,Andrew G. Sharpe,Omer Barad,Kobi Baruch,Gabriel Keeble-Gagnère,Martin Mascher,Gil Ben-Zvi,Ambre-Aurore Josselin,Axel Himmelbach,François Balfourier,Juan J. Gutierrez-Gonzalez,Matthew J. Hayden,Chushin Koh,Gary J. Muehlbauer,Raj K. Pasam,Etienne Paux,Philippe Rigault,Josquin Tibbits,Vijay K. Tiwari,Manuel Spannagl,Daniel Lang,Heidrun Gundlach,Georg Haberer,Klaus F. X. Mayer,Danara Ormanbekova,Verena M. Prade,Hana Šimková,Thomas Wicker,David Swarbreck,Hélène Rimbert,Marius Felder,Nicolas Guilhot,Gemy Kaithakottil,Jens Keilwagen,Philippe Leroy,Thomas Lux,Sven Twardziok,Luca Venturini,Angéla Juhász,Michael Abrouk,Iris Fischer,Cristobal Uauy,Philippa Borrill,Ricardo H. Ramirez-Gonzalez,Dominique Arnaud,Smahane Chalabi,Boulos Chalhoub,Boulos Chalhoub,Aron T. Cory,Raju Datla,Mark W. Davey,John Jacobs,Stephen J. Robinson,Burkhard Steuernagel,Fred van Ex,Brande B. H. Wulff,Moussa Benhamed,Abdelhafid Bendahmane,Lorenzo Concia,David Latrasse,Jan Bartoš,Arnaud Bellec,Hélène Bergès,Jaroslav Doležel,Zeev Frenkel,Bikram S. Gill,Abraham B. Korol,Thomas Letellier,Odd-Arne Olsen,Kuldeep Singh,Miroslav Valárik,Edwin A. G. van der Vossen,Sonia Vautrin,Song Weining,Tzion Fahima,Vladimir Glikson,Dina Raats,Jarmila Číhalíková,Helena Toegelová,Jan Vrána,Pierre Sourdille,Benoit Darrier,D. Barabaschi,Luigi Cattivelli,Pilar Hernández,Sergio Gálvez,Hikmet Budak,Jonathan D. G. Jones,Kamil Witek,Guotai Yu,Ian Small,Joanna Melonek,Ruonan Zhou,Tatiana Belova,Kostya Kanyuka,Robert King,Kirby T. Nilsen,Sean Walkowiak,Richard D. Cuthbert,Ron Knox,Krysta Wiebe,Daoquan Xiang,Antje Rohde,Timothy Golds,Jana Čížková,Bala Ani Akpinar,Sezgi Biyiklioglu,Liangliang Gao,Amidou N’Daiye,Marie Kubaláková,Jan Šafář,Françoise Alfama,Anne-Françoise Adam-Blondon,Raphael Flores,Claire Guerche,Mikaël Loaec,Hadi Quesneville,Janet A. Condie,Jennifer Ens,Ron MacLachlan,Yifang Tan,Adriana Alberti,Jean-Marc Aury,Valérie Barbe,Arnaud Couloux,Corinne Cruaud,Karine Labadie,Sophie Mangenot,Patrick Wincker,Patrick Wincker,Gaganpreet Kaur,Ming-Cheng Luo,Sunish K. Sehgal,Parveen Chhuneja,O. P. Gupta,Suruchi Jindal,Parampreet Kaur,Palvi Malik,Priti Sharma,Bharat Yadav,Nagendra K. Singh,Jitendra P. Khurana,Chanderkant Chaudhary,Paramjit Khurana,Vinod Kumar,Ajay Kumar Mahato,Saloni Mathur,Amitha Mithra Sevanthi,Naveen Sharma,Ram Sewak Singh Tomar,Kateřina Holušová,Ondřej Plíhal,Matthew D. Clark,Matthew D. Clark,Darren Heavens,George Kettleborough,Jon Wright,Barbora Balcárková,Yuqin Hu,Elena A. Salina,Nikolai V. Ravin,Nikolai V. Ravin,Konstantin G. Skryabin,Konstantin G. Skryabin,Alexey V. Beletsky,Vitaly V. Kadnikov,Andrey V. Mardanov,Michail A. Nesterov,Andrey L. Rakitin,Ekaterina M. Sergeeva,Hirokazu Handa,Hiroyuki Kanamori,Satoshi Katagiri,Fuminori Kobayashi,Shuhei Nasuda,Tsuyoshi Tanaka,Jianzhong Wu,Federica Cattonaro,Min Jiumeng,Karl G. Kugler,Matthias Pfeifer,Simen Rød Sandve,Xu Xun,Bujie Zhan,Jacqueline Batley,Philipp E. Bayer,David Edwards,Satomi Hayashi,Zuzana Tulpová,Paul Visendi,Licao Cui,Xianghong Du,Kewei Feng,Xiaojun Nie,Wei Tong,Le Wang +207 more
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Journal ArticleDOI
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Journal ArticleDOI
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