contributors:team_1_page
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contributors:team_1_page [2015/05/03 23:41] jennie [Programs used] |
contributors:team_1_page [2015/07/18 20:29] (current) ceisenhart ↷ Page moved from team_1_page to contributors:team_1_page |
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| =====Team composition===== | =====Team composition===== | ||
| - | | Name | Email| | + | | Name | Email | |
| | Charles Cole | chkcole@ucsc.edu | | | Charles Cole | chkcole@ucsc.edu | | ||
| | Jake Houser | jdhouser@ucsc.edu | | | Jake Houser | jdhouser@ucsc.edu | | ||
| - | | Kyle McGovern | kmcgover@dudek.org | | + | | Kyle McGovern | kmcgover@ucsc.edu | |
| | Jennie Richardson | jemricha@ucsc.edu | | | Jennie Richardson | jemricha@ucsc.edu | | ||
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| After selecting a k-mer set, Meraculous produces a set of maximal linear sub-paths of the deBruijn graph. This process avoids an explicit error correction step used in other assemblers, instead relying on base quality scores. It then aligns reads to the assembly in order to identify useful read-pair information. Next, it uses paired-reads and splinting singletons to produce a scaffolding by “ordering and orienting” a set of contigs. Finally, gaps are closed using paired-end placements. | After selecting a k-mer set, Meraculous produces a set of maximal linear sub-paths of the deBruijn graph. This process avoids an explicit error correction step used in other assemblers, instead relying on base quality scores. It then aligns reads to the assembly in order to identify useful read-pair information. Next, it uses paired-reads and splinting singletons to produce a scaffolding by “ordering and orienting” a set of contigs. Finally, gaps are closed using paired-end placements. | ||
| - | =====Programs used===== | + | =====Other programs used===== |
| ===GCC=== | ===GCC=== | ||
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| ===Skewer=== | ===Skewer=== | ||
| Skewer is an adapter trimmer for Illumina paired-end sequences (/campusdata/BME235/bin/skewer-0.1.123-linux-x86_64). Webpage: http://sourceforge.net/projects/skewer/. | Skewer is an adapter trimmer for Illumina paired-end sequences (/campusdata/BME235/bin/skewer-0.1.123-linux-x86_64). Webpage: http://sourceforge.net/projects/skewer/. | ||
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| + | =====Results===== | ||
| + | We were unable to get Meraculous to complete the bubble popping step. Prior to the assembly being killed, there were 28,610,138 total contigs with 542,137 (1.89%) contigs over 1,000bp and 15 (5.2e-5%) contigs over 10,000bp. | ||
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| + | Our team was dissolved to support other tasks. | ||
| =====Lecture slides===== | =====Lecture slides===== | ||
| {{:bme_235_meraculous_report_1.pdf| First report, Monday April 20th, 2015}} | {{:bme_235_meraculous_report_1.pdf| First report, Monday April 20th, 2015}} | ||
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| + | {{:bme235_meraculous_report_2.pdf| Second report, Monday May 11th, 2015}} | ||
contributors/team_1_page.1430696465.txt.gz · Last modified: 2015/05/03 23:41 by jennie
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