Literature DB >> 26828418

TruSPAdes: barcode assembly of TruSeq synthetic long reads.

Anton Bankevich1, Pavel A Pevzner1,2.   

Abstract

The recently introduced TruSeq synthetic long read (TSLR) technology generates long and accurate virtual reads from an assembly of barcoded pools of short reads. The TSLR method provides an attractive alternative to existing sequencing platforms that generate long but inaccurate reads. We describe the truSPAdes algorithm (http://bioinf.spbau.ru/spades) for TSLR assembly and show that it results in a dramatic improvement in the quality of metagenomics assemblies.

Mesh：

Year:  2016        PMID： 26828418     DOI： 10.1038/nmeth.3737

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  38 in total

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Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

2.  Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.

Authors:  Konstantin Berlin; Sergey Koren; Chen-Shan Chin; James P Drake; Jane M Landolin; Adam M Phillippy
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3.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

Authors:  Chen-Shan Chin; David H Alexander; Patrick Marks; Aaron A Klammer; James Drake; Cheryl Heiner; Alicia Clum; Alex Copeland; John Huddleston; Evan E Eichler; Stephen W Turner; Jonas Korlach
Journal:  Nat Methods       Date:  2013-05-05       Impact factor: 28.547

4.  MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Authors:  Todd J Treangen; Sergey Koren; Daniel D Sommer; Bo Liu; Irina Astrovskaya; Brian Ondov; Aaron E Darling; Adam M Phillippy; Mihai Pop
Journal:  Genome Biol       Date:  2013-01-15       Impact factor: 13.583

5.  Ray Meta: scalable de novo metagenome assembly and profiling.

Authors:  Sébastien Boisvert; Frédéric Raymond; Elénie Godzaridis; François Laviolette; Jacques Corbeil
Journal:  Genome Biol       Date:  2012-12-22       Impact factor: 13.583

6.  Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the "Finished" C. elegans Genome.

Authors:  Runsheng Li; Chia-Ling Hsieh; Amanda Young; Zhihong Zhang; Xiaoliang Ren; Zhongying Zhao
Journal:  Sci Rep       Date:  2015-06-03       Impact factor: 4.379

7.  Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.

Authors:  Rajiv C McCoy; Ryan W Taylor; Timothy A Blauwkamp; Joanna L Kelley; Michael Kertesz; Dmitry Pushkarev; Dmitri A Petrov; Anna-Sophie Fiston-Lavier
Journal:  PLoS One       Date:  2014-09-04       Impact factor: 3.240

8.  How to apply de Bruijn graphs to genome assembly.

Authors:  Phillip E C Compeau; Pavel A Pevzner; Glenn Tesler
Journal:  Nat Biotechnol       Date:  2011-11-08       Impact factor: 54.908

9.  ExSPAnder: a universal repeat resolver for DNA fragment assembly.

Authors:  Andrey D Prjibelski; Irina Vasilinetc; Anton Bankevich; Alexey Gurevich; Tatiana Krivosheeva; Sergey Nurk; Son Pham; Anton Korobeynikov; Alla Lapidus; Pavel A Pevzner
Journal:  Bioinformatics       Date:  2014-06-15       Impact factor: 6.937

10.  LoRDEC: accurate and efficient long read error correction.

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Journal:  Bioinformatics       Date:  2014-08-26       Impact factor: 6.937
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  13 in total

1.  Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

Authors:  Nathan D Olson; Todd J Treangen; Christopher M Hill; Victoria Cepeda-Espinoza; Jay Ghurye; Sergey Koren; Mihai Pop
Journal:  Brief Bioinform       Date:  2019-07-19       Impact factor: 11.622

2.  Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.

Authors:  Dmitry Meleshko; Rui Yang; Patrick Marks; Stephen Williams; Iman Hajirasouliha
Journal:  Nucleic Acids Res       Date:  2022-10-14       Impact factor: 19.160

3.  rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data.

Authors:  Elena Bushmanova; Dmitry Antipov; Alla Lapidus; Andrey D Prjibelski
Journal:  Gigascience       Date:  2019-09-01       Impact factor: 6.524

4.  Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes.

Authors:  Richard Allen White; Eric M Bottos; Taniya Roy Chowdhury; Jeremy D Zucker; Colin J Brislawn; Carrie D Nicora; Sarah J Fansler; Kurt R Glaesemann; Kevin Glass; Janet K Jansson
Journal:  mSystems       Date:  2016-06-28       Impact factor: 6.496

5.  Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters!

Authors:  John Vollmers; Sandra Wiegand; Anne-Kristin Kaster
Journal:  PLoS One       Date:  2017-01-18       Impact factor: 3.240

6.  metaSPAdes: a new versatile metagenomic assembler.

Authors:  Sergey Nurk; Dmitry Meleshko; Anton Korobeynikov; Pavel A Pevzner
Journal:  Genome Res       Date:  2017-03-15       Impact factor: 9.043

7.  Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.

Authors:  Soonok Kim; Yun Sung Cho; Hak-Min Kim; Oksung Chung; Hyunho Kim; Sungwoong Jho; Hong Seomun; Jeongho Kim; Woo Young Bang; Changmu Kim; Junghwa An; Chang Hwan Bae; Youngjune Bhak; Sungwon Jeon; Hyejun Yoon; Yumi Kim; JeHoon Jun; HyeJin Lee; Suan Cho; Olga Uphyrkina; Aleksey Kostyria; John Goodrich; Dale Miquelle; Melody Roelke; John Lewis; Andrey Yurchenko; Anton Bankevich; Juok Cho; Semin Lee; Jeremy S Edwards; Jessica A Weber; Jo Cook; Sangsoo Kim; Hang Lee; Andrea Manica; Ilbeum Lee; Stephen J O'Brien; Jong Bhak; Joo-Hong Yeo
Journal:  Genome Biol       Date:  2016-10-11       Impact factor: 13.583

8.  Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.

Authors:  Zhoutao Chen; Long Pham; Tsai-Chin Wu; Guoya Mo; Yu Xia; Peter L Chang; Devin Porter; Tan Phan; Huu Che; Hao Tran; Vikas Bansal; Justin Shaffer; Pedro Belda-Ferre; Greg Humphrey; Rob Knight; Pavel Pevzner; Son Pham; Yong Wang; Ming Lei
Journal:  Genome Res       Date:  2020-06-15       Impact factor: 9.043

9.  High-quality genome sequences of uncultured microbes by assembly of read clouds.

Authors:  Alex Bishara; Eli L Moss; Mikhail Kolmogorov; Alma E Parada; Ziming Weng; Arend Sidow; Anne E Dekas; Serafim Batzoglou; Ami S Bhatt
Journal:  Nat Biotechnol       Date:  2018-10-15       Impact factor: 54.908

10.  cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.

Authors:  Ivan Tolstoganov; Anton Bankevich; Zhoutao Chen; Pavel A Pevzner
Journal:  Bioinformatics       Date:  2019-07-15       Impact factor: 6.937
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