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teaching:alggrliterature [2022/11/21 09:53]
jstoye [Genome assembly Ib: Re-sequencing, comparative (reference-based) assembly] 		teaching:alggrliterature [2025/11/27 09:08] (current)
jstoye [Transcriptomics I: mRNA analysis, RNA-Seq]
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   - C.-S. Chin, D. H. Alexander, P. Marks, A. A. Klammer, J. Drake, C. Heiner, A. Clum, A. Copeland, J. Huddleston, E. E. Eichler, S. W. Turner, J. Korlach. [[https://​doi.org/​10.1038/​nmeth.2474|Nonhybrid,​ finished microbial genome assemblies from long-read SMRT sequencing data]]. //Nature Methods// **10**:​563-569,​ 2013.   - C.-S. Chin, D. H. Alexander, P. Marks, A. A. Klammer, J. Drake, C. Heiner, A. Clum, A. Copeland, J. Huddleston, E. E. Eichler, S. W. Turner, J. Korlach. [[https://​doi.org/​10.1038/​nmeth.2474|Nonhybrid,​ finished microbial genome assemblies from long-read SMRT sequencing data]]. //Nature Methods// **10**:​563-569,​ 2013.
   - G. Myers. [[https://​doi.org/​10.1007/​978-3-662-44753-6_5|Efficient Local Alignment Discovery amongst Noisy Long Reads]]. //​Proceedings of WABI 2014//, LNBI 8701, 52-67, 2014.   - G. Myers. [[https://​doi.org/​10.1007/​978-3-662-44753-6_5|Efficient Local Alignment Discovery amongst Noisy Long Reads]]. //​Proceedings of WABI 2014//, LNBI 8701, 52-67, 2014.
 +  - F. J. Sedlazeck, P. Rescheneder,​ M. Smolka, H. Fang, M. Nattestad, A. von Haeseler, M. C. Schatz. [[https://​doi.org/​10.1038/​s41592-018-0001-7|Accurate detection of complex structural variations using single molecule sequencing]]. //Nat. Methods// **15**(6): 461–468, 2018.
   - E. Haghshenas, H. Asghari, J. Stoye, C. Chauve, F. Hach. [[https://​doi.org/​10.1016/​j.isci.2020.101389|HASLR:​ Fast Hybrid Assembly of Long Reads]]. //​iScience//​ **23**(8): 101389, 2020.   - E. Haghshenas, H. Asghari, J. Stoye, C. Chauve, F. Hach. [[https://​doi.org/​10.1016/​j.isci.2020.101389|HASLR:​ Fast Hybrid Assembly of Long Reads]]. //​iScience//​ **23**(8): 101389, 2020.
  
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 |Splicing graphs and EST assembly problem]]. //​Bioinformatics//​ **18**(Suppl. 1):​S181-S188,​ 2002.  |Splicing graphs and EST assembly problem]]. //​Bioinformatics//​ **18**(Suppl. 1):​S181-S188,​ 2002. 
   - M. Sammeth, S. Foissac, R. Guigó. [[https://​doi.org/​10.1371/​journal.pcbi.1000147|A general definition and nomenclature for alternative splicing events]]. //PLoS Comput. Biol.// **4**(8):​e1000147,​ 2008.    - M. Sammeth, S. Foissac, R. Guigó. [[https://​doi.org/​10.1371/​journal.pcbi.1000147|A general definition and nomenclature for alternative splicing events]]. //PLoS Comput. Biol.// **4**(8):​e1000147,​ 2008. 
-  - V. Lacroix, M. Sammeth, R. Guigó, A. Bergeron. [[https://​doi.org/​10.1007/​978-3-540-87361-7_5|Exact Transcriptome Reconstruction from Short Sequence reads]]. Proc. WABi 2008, LNBI 5251, 50-63, 2008. +  - V. Lacroix, M. Sammeth, R. Guigó, A. Bergeron. [[https://​doi.org/​10.1007/​978-3-540-87361-7_5|Exact Transcriptome Reconstruction from Short Sequence reads]]. Proc. WABI 2008, LNBI 5251, 50-63, 2008. 
  
 Very good review about NGS transcriptomics (RNA-seq): ​ Very good review about NGS transcriptomics (RNA-seq): ​