lecture_notes:04-20-2015
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lecture_notes:04-20-2015 [2015/04/25 02:55] calef [Basic features] |
lecture_notes:04-20-2015 [2015/04/25 03:04] calef [User experience] |
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| * Counts occurrences of each kmer in the data set. | * Counts occurrences of each kmer in the data set. | ||
| - | * Removes kmers whose frequency are below the user threshold. | + | * Removes kmers whose frequency are below a threshold provided by the user. |
| * For each kmer, counts the number of high-quality single-base extensions | * For each kmer, counts the number of high-quality single-base extensions | ||
| - | * Classifies the 5' and 3' ends of each kmer | + | * Classifies the 5' and 3' ends of each kmer as U, F, or X, corresponding to having zero, one, or multiple high-quality single-base extensions |
| * Stores the extensions of kmers with a classification in a hash | * Stores the extensions of kmers with a classification in a hash | ||
| - | * Removes non-reciprocal linkages between kmers | + | * Removes non-reciprocal U-U extensions between kmers (i.e. an extension where the end of one mer is marked as U but the other is marked F). |
| + | * Stores the linear subgraph of U-U extensions | ||
| * Selects kmers at random and extend outwards to produce contigs | * Selects kmers at random and extend outwards to produce contigs | ||
| * Aligns all reads to contigs via BLAST | * Aligns all reads to contigs via BLAST | ||
| * Assembles contigs into scaffolds using paired-end data | * Assembles contigs into scaffolds using paired-end data | ||
| * Searches unaligned reads as potential gap-closers using mate-pair data | * Searches unaligned reads as potential gap-closers using mate-pair data | ||
| - | |||
| =====Meraculous limitations===== | =====Meraculous limitations===== | ||
| - | * The assembler relies on data with high quality in order to avoid error correction | + | * The assembler relies on data with high quality in order to avoid error correction, also requires high coverage |
| * Initial release did not support polyploid genome assembly due to allowing for linear subgraphs of the de Bruijn graph only | * Initial release did not support polyploid genome assembly due to allowing for linear subgraphs of the de Bruijn graph only | ||
| - | * Low memory footprint | + | * High disk space usage |
| =====User experience===== | =====User experience===== | ||
| * Requires an array of other scripts in other languages | * Requires an array of other scripts in other languages | ||
| * Most of high level scripts are written in perl | * Most of high level scripts are written in perl | ||
| - | * Tested the program in small dataset and obtained contigs | + | * Tested the program with the packaged test data and obtained contigs |
| =====Installation===== | =====Installation===== | ||
| - | * Main issue was get all dependencies together | + | * Main issue was new version of GCC and getting all the dependencies together ~16 hrs |
| - | * There was one non-standard perl mode needed | + | * There was one non-standard perl module needed |
| + | * Files with carriage returns | ||
| * Some scripts contain error but they aren't hard to fix. | * Some scripts contain error but they aren't hard to fix. | ||
| =====Running Meraculous===== | =====Running Meraculous===== | ||
lecture_notes/04-20-2015.txt · Last modified: 2015/04/25 03:07 by calef
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