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teaching:alggrliterature [2022/01/27 13:57] – [Computational pangenomics] jstoyeteaching:alggrliterature [2025/11/27 08:08] (current) – [Transcriptomics I: mRNA analysis, RNA-Seq] jstoye
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 ==== Genome assembly Ib: Re-sequencing, comparative (reference-based) assembly ==== ==== Genome assembly Ib: Re-sequencing, comparative (reference-based) assembly ====
-A good introduction to comparative genome assembly is [1]. The main algorithmic challenge is to map millions of (most very short) sequence reads onto one or more referene geneome(s). Suitable mapping algorithms for this task are [[http://bibiserv.cebitec.uni-bielefeld.de/swift/|SWIFT]] [2], [[http://bowtie-bio.sourceforge.net/index.shtml|Bowtie]] [6], ELAND (Cox, unpublished), [[http://maq.sourceforge.net/|MAQ]] [3], [[http://rulai.cshl.edu/rmap/|RMAP]], [[http://soap.genomics.org.cn/|SOAP]] [4], [[http://compbio.cs.toronto.edu/shrimp/|SHRiMP]], SeqMap [5], TAGGER [7], ZOOM [8], [[http://bio-bwa.sourceforge.net/bwa.shtml|BWA]] [9], GSNAP [10], SARUMAN [11], SSAHA2 [12] etc. Methods especially suited for mapping SOLiD reads are presented in [13,14]. +A good introduction to comparative genome assembly is [1]. The main algorithmic challenge is to map millions of (most very short) sequence reads onto one or more referene geneome(s). Suitable mapping algorithms for this task are [[http://bibiserv.cebitec.uni-bielefeld.de/swift/|SWIFT]] [2], [[http://bowtie-bio.sourceforge.net/index.shtml|Bowtie]] [6], ELAND (Cox, unpublished), [[http://maq.sourceforge.net/|MAQ]] [3], [[http://rulai.cshl.edu/rmap/|RMAP]], [[http://soap.genomics.org.cn/|SOAP]] [4], [[http://compbio.cs.toronto.edu/shrimp/|SHRiMP]], SeqMap [5], TAGGER [7], ZOOM [8], [[http://bio-bwa.sourceforge.net/bwa.shtml|BWA]] [9], GSNAP [10], SARUMAN [11], SSAHA2 [12], NextGenMap [13], etc.
  
   - M. Pop, A. Phillippy, A. L. Delcher, and S. L. Salzberg. [[https://doi.org/10.1093/bib/5.3.237|Comparative genome assembly]]. //Briefings in Bioinformatics// **5**(3):237-248, 2004.    - M. Pop, A. Phillippy, A. L. Delcher, and S. L. Salzberg. [[https://doi.org/10.1093/bib/5.3.237|Comparative genome assembly]]. //Briefings in Bioinformatics// **5**(3):237-248, 2004. 
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   - J. Blom, T. Jakobi, D. Doppmeier, S. Jaenicke, J. Kalinowski, J. Stoye, A. Goesmann. [[https://doi.org/10.1093/bioinformatics/btr151|Exact and complete short read alignment to microbial genomes using GPU programming]]. //Bioinformatics// **27**(10): 1351-1358, 2011.    - J. Blom, T. Jakobi, D. Doppmeier, S. Jaenicke, J. Kalinowski, J. Stoye, A. Goesmann. [[https://doi.org/10.1093/bioinformatics/btr151|Exact and complete short read alignment to microbial genomes using GPU programming]]. //Bioinformatics// **27**(10): 1351-1358, 2011. 
   - Z. Ning, A.J. Cox. [[https://doi.org/10.1101/gr.194201|SSAHA: A Fast Search Method for Large DNA Databases]]. //Genome Res.// **11**(10): 1725-1729, 2001.    - Z. Ning, A.J. Cox. [[https://doi.org/10.1101/gr.194201|SSAHA: A Fast Search Method for Large DNA Databases]]. //Genome Res.// **11**(10): 1725-1729, 2001. 
-  - L. Noé, M. Gîrdea, G. Kucherov. [[https://doi.org/10.1007/978-3-642-12683-3_25|Seed Design Framework for Mapping SOLiD Reads]]. Proceedings of RECOMB 2010, LNBI 6044, 384-396, 2010.  +  - F. J. Sedlazeck, P. Rescheneder, A. von Haeseler. [[https://doi.org/10.1093/bioinformatics/btt468|NextGenMap: fast and accurate read mapping in highly polymorphic genomes]]. //Bioinformatics// **29**(21): 2790-2791, 2013.
-  - M. Csűrös, Sz. Juhos, A. Bérces. [[https://doi.org/10.1007/978-3-642-15294-8_15|Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA]]. Proceedings of WABI 2010, LNBI 6293, 176-188, 2010. +
   - L. Oesper, A. Ritz, S. J. Aerni, R. Drebin, B. J. Raphael. [[https://doi.org/10.1186/1471-2105-13-S6-S10|Reconstructing cancer genomes from paired-end sequencing data]]. //BMC Bioinformatics// **13**(Suppl. 6):S10, 2012.    - L. Oesper, A. Ritz, S. J. Aerni, R. Drebin, B. J. Raphael. [[https://doi.org/10.1186/1471-2105-13-S6-S10|Reconstructing cancer genomes from paired-end sequencing data]]. //BMC Bioinformatics// **13**(Suppl. 6):S10, 2012. 
  
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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): 
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