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--- teaching:alggrliterature [2022/01/27 14:57]
jstoye [Computational pangenomics]
+++ teaching:alggrliterature [2022/11/21 09:53]
jstoye [Genome assembly Ib: Re-sequencing, comparative (reference-based) assembly]
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 ==== 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[2], [[http://bowtie-bio.sourceforge.net/index.shtml|Bowtie]] [6], ELAND (Cox, unpublished), [[http://maq.sourceforge.net/|MAQ]] [3], [[http://rulai.cshl.edu/rmap/|RMAP]], [[http://soap.genomics.org.cn/|SOAP]] [4],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[2], [[http://bowtie-bio.sourceforge.net/index.shtml|Bowtie]] [6], ELAND (Cox, unpublished), [[http://maq.sourceforge.net/|MAQ]] [3], [[http://rulai.cshl.edu/rmap/|RMAP]], [[http://soap.genomics.org.cn/|SOAP]] [4],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.
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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.
   - 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.

Genome Informatics

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