archive:computer_resources:assemblies
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
archive:computer_resources:assemblies [2011/06/21 23:27] karplus [slug/] moved mitochondrion assembly information to a new page |
archive:computer_resources:assemblies [2015/09/02 16:53] 92.247.181.31 ↷ Links adapted because of a move operation |
||
|---|---|---|---|
| Line 19: | Line 19: | ||
| * newbler-assembly2/ is a second de novo assembly using Newbler, starting from the cleaned reads of newbler-clean1/sff_cleaned/no_Hyp.sff It gets 42 contigs and 2,449,409 bases. | * newbler-assembly2/ is a second de novo assembly using Newbler, starting from the cleaned reads of newbler-clean1/sff_cleaned/no_Hyp.sff It gets 42 contigs and 2,449,409 bases. | ||
| * newbler-assembly3/ starts from the same sff file as newbler-assembly2/ but raises the expected coverage to 60 (close to actual coverage). It gets 41 contigs and 2,449,426 bases, still more than the old version of Newbler got after similar cleaning. The contigs have been mapped to the finished genome (using megablast, blastn, blat, and pluck-scripts/find-dna-differences). All the contigs map cleanly to the finished genome. If contigs map to more than one place, find-dna-differences may (incorrectly) report it as not mapping. | * newbler-assembly3/ starts from the same sff file as newbler-assembly2/ but raises the expected coverage to 60 (close to actual coverage). It gets 41 contigs and 2,449,426 bases, still more than the old version of Newbler got after similar cleaning. The contigs have been mapped to the finished genome (using megablast, blastn, blat, and pluck-scripts/find-dna-differences). All the contigs map cleanly to the finished genome. If contigs map to more than one place, find-dna-differences may (incorrectly) report it as not mapping. | ||
| - | * map-colorspace3/ uses the [[bioinformatic_tools:pluck-scripts|pluck-scripts]] script map-colorspace to map the SOLiD mate-pair reads onto the contigs of the newbler-assembly3/ run. The intent is to find what contigs join to what other ones. The numbering starts with 3, not 1, so that the map-colorspace directories correspond to the newbler-assembly directories that they are mapping onto. | + | * map-colorspace3/ uses the [[archive:bioinformatic_tools:pluck-scripts|pluck-scripts]] script map-colorspace to map the SOLiD mate-pair reads onto the contigs of the newbler-assembly3/ run. The intent is to find what contigs join to what other ones. The numbering starts with 3, not 1, so that the map-colorspace directories correspond to the newbler-assembly directories that they are mapping onto. |
| * newbler-partial3/ assembled the partially-assembled reads of newbler-assembly3/ to see if any extended or connected contigs. Seven of the 131 new contigs could be used to extend newbler-assembly3/ contigs, but none spanned 2 contigs. | * newbler-partial3/ assembled the partially-assembled reads of newbler-assembly3/ to see if any extended or connected contigs. Seven of the 131 new contigs could be used to extend newbler-assembly3/ contigs, but none spanned 2 contigs. | ||
| * newbler-assembly4/ starts from the same sff file as newbler-assembly2/ and newbler-assembly3/ but adds the contigs of newbler-partial3/ as extra reads. This did not help, getting 45 contigs and 2,449,287 bases. | * newbler-assembly4/ starts from the same sff file as newbler-assembly2/ and newbler-assembly3/ but adds the contigs of newbler-partial3/ as extra reads. This did not help, getting 45 contigs and 2,449,287 bases. | ||
| Line 29: | Line 29: | ||
| * euler-sr-assembly1/ | * euler-sr-assembly1/ | ||
| * mira | * mira | ||
| - | * [[computer_resources:assemblies:mira:pog:mira-assembly1|]] | + | * [[archive:computer_resources:assemblies:mira:pog:mira-assembly1]] |
| - | * [[computer_resources:assemblies:mira:pog:mira-assembly2|]] | + | * [[archive:computer_resources:assemblies:mira:pog:mira-assembly2]] |
| * velvet | * velvet | ||
| * velvet-assembly1/ Assembling Pog 454 long reads with velvet. After very poor results with default settings, eventually started to get good results by getting the expected coverage (60) and cutoff (13) correct. It took a long time try different parameter settings. Also using the long reads as both short and long reads gave substantially better results. Because these were long reads, we could set k up to 31. Also tried with specially compiled version of velvet that could use k > 31, but can not report any improvement yet. Given that the average read is 370b, it should have been able to support longer k-values. Best results so far:\\ | * velvet-assembly1/ Assembling Pog 454 long reads with velvet. After very poor results with default settings, eventually started to get good results by getting the expected coverage (60) and cutoff (13) correct. It took a long time try different parameter settings. Also using the long reads as both short and long reads gave substantially better results. Because these were long reads, we could set k up to 31. Also tried with specially compiled version of velvet that could use k > 31, but can not report any improvement yet. Given that the average read is 370b, it should have been able to support longer k-values. Best results so far:\\ | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
