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--- archive:computer_resources:assemblies [2010/04/22 12:29]
karplus Added T-shirt k-mer suggestion.
+++ archive:computer_resources:assemblies [2010/04/22 13:28]
karplus corrected order of short repeats (using double-stranded counts)
@@ Line 37: / Line 37: @@
 ===== slug/ =====
-  * 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.  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.)  Much of the assembly is low-complexity regions (repetitions of short repeats (GA)*, (TA)*, (TTC)*, (AC)*, (TAG)*, (CGAA)*, (TATC)*, (CAA)*, ... ).  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).
+  * 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.  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.)  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).

Banana Slug Genomics

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