lecture_notes:04-26-2010
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lecture_notes:04-26-2010 [2010/04/26 22:22] hyjkim created |
lecture_notes:04-26-2010 [2010/04/28 20:56] (current) galt |
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| Galt's lecture on velvet | Galt's lecture on velvet | ||
| * A lot of parameters with velvet to work with | * A lot of parameters with velvet to work with | ||
| - | * Easy to install compared to other tools like allopaths | + | * Easy to install compared to other tools like allpaths |
| * /campus/BME235/programs/velvet/ is the home directory | * /campus/BME235/programs/velvet/ is the home directory | ||
| * To install, simply type 'make' | * To install, simply type 'make' | ||
| * Copy binaries | * Copy binaries | ||
| * Can change the max-kmer maximum size at compilation | * Can change the max-kmer maximum size at compilation | ||
| - | * 31mers are max six for a 64-bit word | + | * 31mers are max size for a 64-bit word |
| - | * Can add solid support by adding in a "de" tag for double-encoded | + | * Can add solid support by adding in a "_de" tag for double-encoded. |
| - | * Velvet is one of the only tools supporting colorspace reads | + | * Velvet is one of the only de-novo assembly tools supporting colorspace reads |
| * ~velvet/data | * ~velvet/data | ||
| * Contains a simulated genome with simulated reads which can be used for testing the data | * Contains a simulated genome with simulated reads which can be used for testing the data | ||
| - | * No documentation which describes the files within this diretory | + | * No documentation describes the files within this directory |
| * ~velvet/contrib -- Contributors directory | * ~velvet/contrib -- Contributors directory | ||
| - | * estimate-exp_cov -- Estimates expected coverage | + | * velvet-estimate-coverage.pl -- Estimates expected coverage |
| * Maybe reading the stats.txt file which velvet produces | * Maybe reading the stats.txt file which velvet produces | ||
| * VelvetOptimiser-2.1.0 | * VelvetOptimiser-2.1.0 | ||
| * Written to try to find the best parameters for assembling the genome | * Written to try to find the best parameters for assembling the genome | ||
| + | * Did not work, got stuck on local maximum for exp_cov and cov_cutoff | ||
| * ~assemblies/Pog/velvet-assembly1 | * ~assemblies/Pog/velvet-assembly1 | ||
| * Run velvet without any arguments under the assumption that velvet with estimate some correct parameters | * Run velvet without any arguments under the assumption that velvet with estimate some correct parameters | ||
| * README | * README | ||
| - | * Ran without using any quality values. | + | * Ran without using any quality values. Velvet does not use quality values even if using fastq input files. |
| - | * May take quality values from .qual values | + | |
| * Runs in 5-8 minutes | * Runs in 5-8 minutes | ||
| * First estimated coverage and cutoff values were terrible. | * First estimated coverage and cutoff values were terrible. | ||
lecture_notes/04-26-2010.1272320563.txt.gz · Last modified: 2010/04/26 22:22 by hyjkim
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