archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/04/22 20:25] karplus added newbler mapping assemblies |
archive:computer_resources:assemblies [2010/04/22 20:27] karplus added largest contig size for newbler-assembly1 |
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| * newbler-assembly1/ first attempt at de novo assembly using Newbler, using all the reads from 454_run1 and 454_run2. | * newbler-assembly1/ first attempt at de novo assembly using Newbler, using all the reads from 454_run1 and 454_run2. | ||
| - | * This assembly of 499,873 reads including 138,351,643 bases produced only 2,910,773 bases assembled into 8,963 contigs. | + | * This assembly of 499,873 reads including 138,351,643 bases produced only 2,910,773 bases assembled into 8,963 contigs. |
| - | * From this low assembly number, I estimate the coverage to be about 0.043x and the genome size to be about 3.2E9 basepairs. (See the README file for the calculation.) | + | * The longest contig is 5783 bases. |
| + | * From the total number of bases in the assembly number, I estimate the coverage to be about 0.043x and the genome size to be about 3.2E9 basepairs. (See the README file for the calculation.) | ||
| * Much of the assembly is low-complexity regions (repetitions of short repeats (AT)*, (AAG)*, (AG)*, (AC)*, (AGT)*, (AGAT)*, (ACAT)*, (AAC)*, (AACG)*, ... ). | * Much of the assembly is low-complexity regions (repetitions of short repeats (AT)*, (AAG)*, (AG)*, (AC)*, (AGT)*, (AGAT)*, (ACAT)*, (AAC)*, (AACG)*, ... ). | ||
| * The most common 14-mer that is not a repeat of a short k-mer is TAGTTTACAGCTTG (so that is what we should put on the T-shirt). | * The most common 14-mer that is not a repeat of a short k-mer is TAGTTTACAGCTTG (so that is what we should put on the T-shirt). | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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