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teaching:alggrliterature [2022/11/21 09:51]
jstoye [Genome assembly Ib: Re-sequencing, comparative (reference-based) assembly] 		teaching:alggrliterature [2022/11/21 09:57] (current)
jstoye [Genome assembly IIb: Hybrid/long read assembly]
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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[2], [[http://​bowtie-bio.sourceforge.net/​index.shtml|Bowtie]] [6], ELAND (Cox, unpublished),​ [[http://​maq.sourceforge.net/​|MAQ]] [3], [[http://​rulai.cshl.edu/​rmap/​|RMAP]],​ [[http://​soap.genomics.org.cn/​|SOAP]] [4],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[2], [[http://​bowtie-bio.sourceforge.net/​index.shtml|Bowtie]] [6], ELAND (Cox, unpublished),​ [[http://​maq.sourceforge.net/​|MAQ]] [3], [[http://​rulai.cshl.edu/​rmap/​|RMAP]],​ [[http://​soap.genomics.org.cn/​|SOAP]] [4],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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   - 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.