lecture_notes:04-26-2015
Differences
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lecture_notes:04-26-2015 [2015/04/29 07:18] gepoliano created |
lecture_notes:04-26-2015 [2015/04/29 20:25] 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===== | ||
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| =====Workflow===== | =====Workflow===== | ||
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| * 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 | ||
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| + | =====ABySS Details===== | ||
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| + | * 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 | ||
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| + | =====Installing ABySS===== | ||
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| + | * 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 | ||
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lecture_notes/04-26-2015.txt ยท Last modified: 2015/04/29 20:25 by jdhouser
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