contributors:team_1_page
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contributors:team_1_page [2015/05/03 23:18] jennie created |
contributors:team_1_page [2015/05/03 23:46] jennie [Programs used] |
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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===== |
| - | The program, its location, and a brief explanation of what the program does | + | |
| - | + | ||
| - | ===Skewer=== | + | |
| - | Skewer is an adapter trimmer for Illumina paired-end sequences (/campusdata/BME235/S15_assemblies/SOAPdenovo2/adapterRemovalTask/skewer_run). Webpage: http://sourceforge.net/projects/skewer/. | + | |
| ===GCC=== | ===GCC=== | ||
| - | GCC is a compiler for the GNU operating system (/campusdata/BME235/bin). Webpage: https://gcc.gnu.org/. | + | GCC is a compiler for the GNU operating system (/campusdata/BME235/bin/gcc-4.9.2). Webpage: https://gcc.gnu.org/. |
| + | |||
| + | ===KmerGenie=== | ||
| + | KmerGenie estimates the best k-mer length for genome //de novo// assembly (/campusdata/BME235/bin/kmergenie-1.6972). Webpage: http://kmergenie.bx.psu.edu/. | ||
| + | |||
| + | ===Musket=== | ||
| + | Musket is a multistage k-mer spectrum based error corrector for Illumina short read data (/campusdata/BME235/bin/musket). Webpage: http://musket.sourceforge.net/. | ||
| + | |||
| + | ===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/. | ||
contributors/team_1_page.txt · Last modified: 2015/07/18 20:29 by ceisenhart
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