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lecture_notes:04-26-2015

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lecture_notes:04-26-2015 [2015/04/29 00:18]
gepoliano created
lecture_notes:04-26-2015 [2015/04/29 13:25] (current)
jdhouser Merged my notes in
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 ======Team 4 Report: ABySS====== ======Team 4 Report: ABySS======
-ABySS stands for Assembly ​by short sequences.+ABySS stands for Assembly ​By Short Sequences.
  
 =====Assembler Overview===== =====Assembler Overview=====
Line 10: Line 10:
  
 =====Workflow===== =====Workflow=====
- 
  
   * Generate paths through the reads   * Generate paths through the reads
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       - Maximum Likelihood Estimator       - Maximum Likelihood Estimator
       - Use empirical paired-end size distribution       - Use empirical paired-end size distribution
 +
 +
 +=====ABySS Details=====
 +
 +  * Distributes k-mers and deBruijn graph across a cluster
 +  * Each node announces the list of k-mers it has to nodes that hold their possible extensions
 +  * 8 bits of storage per k-mer, ACGT forward and reverse extensions
 +  * Finds paths through contigs that agree with distance estimates and then merge overlapping paths
 +
 +
 +=====Installing ABySS=====
 +
 +  * Installation of single processor version was straightforward
 +  * Difficulty installing parallelized version
 +  * Developers are active in the community and the assembler has a long history, so documentation is abundant
  
 =====Running ABySS===== =====Running ABySS=====
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   * Run adapter trimming plus merging   * Run adapter trimming plus merging
  
-====Initil ​run====+====Initial ​run====
   * The initial run is located on Edser   * The initial run is located on Edser
   * K = 55, arbitrary   * K = 55, arbitrary
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   * RNA-seq rescaffolding with TransABySS   * RNA-seq rescaffolding with TransABySS
   * Meta-assembly   * Meta-assembly
- 
- 
lecture_notes/04-26-2015.1430291926.txt.gz ยท Last modified: 2015/04/29 00:18 by gepoliano