Graph analysis of fragmented long-read bacterial genome assemblies
暂无分享,去创建一个
[1] Michael Roberts,et al. The MaSuRCA genome assembler , 2013, Bioinform..
[2] Chengxi Ye,et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies , 2014, Scientific Reports.
[3] Anton Nekrutenko,et al. Understanding trivial challenges of microbial genomics: An assembly example , 2018, bioRxiv.
[4] Daniel D. Sommer,et al. De novo likelihood-based measures for comparing genome assemblies , 2013, BMC Research Notes.
[5] M. Schatz,et al. Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.
[6] Justin Zobel,et al. Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.
[7] Eugene W. Myers,et al. The fragment assembly string graph , 2005, ECCB/JBI.
[8] Steven D. Brown,et al. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies , 2017, Front. Microbiol..
[9] Yu Lin,et al. Assembly of Long Error-Prone Reads Using de Bruijn Graphs , 2016 .
[10] S. Lonardi,et al. A comparative evaluation of genome assembly reconciliation tools , 2017, Genome Biology.
[11] Marghoob Mohiyuddin,et al. LongISLND: in silico sequencing of lengthy and noisy datatypes , 2016, Bioinform..
[12] N. Loman,et al. A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.
[13] Pietro Liò,et al. MeDuSa: a multi-draft based scaffolder , 2015, Bioinform..
[14] Ryan R. Wick,et al. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.
[15] Christina A. Cuomo,et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.
[16] Zhong Wang,et al. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies , 2013, Bioinform..
[17] S. Koren,et al. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. , 2015, Current opinion in microbiology.
[18] Dmitry Antipov,et al. hybridSPAdes: an algorithm for hybrid assembly of short and long reads , 2016, Bioinform..
[19] M. Schatz,et al. Genome assembly forensics: finding the elusive mis-assembly , 2008, Genome Biology.
[20] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[21] Sergey Koren,et al. Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..
[22] F. Kremer,et al. Approaches for in silico finishing of microbial genome sequences , 2017, Genetics and molecular biology.
[23] Bud Mishra,et al. Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons , 2012, PloS one.
[24] David Tse,et al. Optimal assembly for high throughput shotgun sequencing , 2013, BMC Bioinformatics.
[25] Heng Li,et al. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences , 2015, Bioinform..
[26] Sergey Koren,et al. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes , 2019, Briefings Bioinform..
[27] Sven Rahmann,et al. Genome analysis , 2022 .
[28] J. Parkhill,et al. Circlator: automated circularization of genome assemblies using long sequencing reads , 2015, bioRxiv.
[29] S. Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[30] Connor T. Skennerton,et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.
[31] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[32] M. Berriman,et al. REAPR: a universal tool for genome assembly evaluation , 2013, Genome Biology.
[33] Ilan Shomorony,et al. HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution , 2016, bioRxiv.
[34] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[35] L. Pachter,et al. CGAL: computing genome assembly likelihoods , 2013 .
[36] M. Touchon,et al. Genesis, effects and fates of repeats in prokaryotic genomes. , 2009, FEMS microbiology reviews.