archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/05/19 20:48] galt |
archive:computer_resources:assemblies [2010/06/06 22:16] galt adding Ray, ABySS, and PCAP on Pog from README |
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| * 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:\\ | ||
| * Final graph has 2176 nodes {195 contigs over 62b) and n50 of 224364, max {contig size} 680241, total {genome size} 2481051, using 778249/782604 reads | * Final graph has 2176 nodes {195 contigs over 62b) and n50 of 224364, max {contig size} 680241, total {genome size} 2481051, using 778249/782604 reads | ||
| + | * velvet-assembly1a/ Assembling Pog 454 long reads with velvet. This is just re-running velvet-assembly1 with the best parameters found and also using kevin's makefile adapted to the velvet data. | ||
| * velvet-assembly2/ Assembling Pog Solid mate-paired 25b reads with velvet in double-encoded colorspace (24 DE base reads). Not had time to optimize parameters yet. Did get up to a max-contig size of 95k. | * velvet-assembly2/ Assembling Pog Solid mate-paired 25b reads with velvet in double-encoded colorspace (24 DE base reads). Not had time to optimize parameters yet. Did get up to a max-contig size of 95k. | ||
| * velveth_de out 21 -shortPaired /campusdata/BME235/data/Pog/solid_run/paired/output/doubleEncoded_input.de | * velveth_de out 21 -shortPaired /campusdata/BME235/data/Pog/solid_run/paired/output/doubleEncoded_input.de | ||
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| * Final graph has 3602 nodes and n50 of 4851, max 94854, total 1767903, using 28785664/61262410 reads | * Final graph has 3602 nodes and n50 of 4851, max 94854, total 1767903, using 28785664/61262410 reads | ||
| * SOAPdenovo | * SOAPdenovo | ||
| - | * SOAPdenovo-assembly1/ Assembling Pog 454 long reads with SOAPdenovo. After being simply unable to get any version of the program to read a FASTA file despite documentation examples, I finally found a utility sff2fastq that made it possible to run SOAPdenovo on Pog 454 fastq. I have not had time to optimize parameters yet. The largest contig made with default params was just 4k. Later raised cutoff to 12 and got maxcontig of 70k. Could not run the scaffold step because it crashed, probably because it was written for short 52bp solexa reads and the long 454 reads are messing it up. | + | * SOAPdenovo-assembly1/ Assembling Pog 454 long reads with SOAPdenovo. After being simply unable to get any version of the program to read a FASTA file despite documentation examples, I finally found a utility sff2fastq that made it possible to run SOAPdenovo on Pog 454 fastq. I have not had time to optimize parameters yet. The largest contig made with default params was just 4k. Later raised cutoff to 12 and got maxcontig of 70k. Could not run the scaffold step because there are no paired libs in this data set. |
| + | * Ray | ||
| + | * Ray-assembly1/ | ||
| + | |||
| + | Assembling Pog 454 long reads with Ray, | ||
| + | a parallel implementation of the OpenAssembler. | ||
| + | This software seems to be Canadian. | ||
| + | It took 3 hours to run, and the output was | ||
| + | not very good, max contig size being about 12k. | ||
| + | Sadly there are no parameters to tweak. | ||
| + | |||
| + | * ABySS | ||
| + | * abyss-assembly1/ | ||
| + | |||
| + | Assembling Pog454 long reads with ABySS. | ||
| + | The best params found were kmer size 36 and coverage cutoff 15 | ||
| + | #ABYSS -k 36 -c 15 both.fq | ||
| + | #Total size: mean 1844.8 sd 3479.7 min 36 (1179) max 32566 (556) median 204 | ||
| + | |||
| + | * PCAP | ||
| + | * pcap-assembly1/ | ||
| + | |||
| + | Assembled Pog 454 long reads with pcap default parameters. Sanger reads are not included. | ||
| + | It was necessary to increase the minimum depth coverage for repeats before we got anything good. | ||
| + | Assembled Pog 454 long reads with minimum depth coverage for repeats set to 200, and rest of the parameters unmodified. | ||
| + | faSize contigs.bases info : | ||
| + | 2506151 bases (8 N's 2506143 real 2506143 upper 0 lower) in 219 sequences in 1 files | ||
| + | Total size: mean 11443.6 sd 65849.3 min 56 (Contig174.1) max 611479 (Contig0.1) median 195 | ||
| + | N count: mean 0.0 sd 0.2 | ||
| + | U count: mean 11443.6 sd 65849.3 | ||
| + | Using Kevin's makefile, the blat alignments showed large contigs that looked basically correct. | ||
| + | However many of them overlapped, unlike the Newbler output. This may have been due to a | ||
| + | difference in the way Newbler and PCAP tried to handle the mixed population in the sample where | ||
| + | 3 inverting regions are found with various frequencies. | ||
| + | Also, a cutoff should probably be supplied somewhere after the 17th largest contig because | ||
| + | most of the rest of the 219 was small contigs probably representing noise. | ||
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| * It was used to assemble the Panda genome by BGI. | * It was used to assemble the Panda genome by BGI. | ||
| * Used kolossus which has 1TB and 64cpus. | * Used kolossus which has 1TB and 64cpus. | ||
| - | * Ran with k=31 an k=23. k=31 was better (9k maxcontig) | + | * Ran with k=31 and k=23. k=31 was better (9k maxcontig) |
| * so ran with filling -R to get 12k maxcontig. | * so ran with filling -R to get 12k maxcontig. | ||
| * Then ran the scaffolding steps with 200bp insert size. | * Then ran the scaffolding steps with 200bp insert size. | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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