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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 09:53]
jstoye [Genome assembly Ib: Re-sequencing, comparative (reference-based) 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[2], [[http://​bowtie-bio.sourceforge.net/​index.shtml|Bowtie]] [6], ELAND (Cox, unpublished),​ [[http://​maq.sourceforge.net/​|MAQ]] [3], [[http://​rulai.cshl.edu/​rmap/​|RMAP]],​ [[http://​soap.genomics.org.cn/​|SOAP]] [4],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[2], [[http://​bowtie-bio.sourceforge.net/​index.shtml|Bowtie]] [6], ELAND (Cox, unpublished),​ [[http://​maq.sourceforge.net/​|MAQ]] [3], [[http://​rulai.cshl.edu/​rmap/​|RMAP]],​ [[http://​soap.genomics.org.cn/​|SOAP]] [4],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.