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--- archive:computer_resources:assemblies [2010/04/23 07:52]
galt
+++ archive:computer_resources:assemblies [2010/06/06 21:45]
galt adding velvet-assembly1a
@@ Line 23: / Line 23: @@
     * 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-assembly5/ starts from the same sff file as newbler-assembly2,3,4 but adds 45 Sanger reads totalling 44,187 bases from PCR reactions (mainly designed to test contig-join hypotheses). It gets 31 contigs and 2,451,007 bases.
-    * map-colorspace5/ maps the SOLiD mate-pair data onto the contigs of newbler-assembly5/  Other than some problems placing contig4 and the ece insertions, we can reconstruct some pretty large chunks of the genome from the mate-pair ends.
+    * map-colorspace5/ maps the SOLiD mate-pair data onto the contigs of newbler-assembly5/  Other than some problems placing contig4 and the ece insertions, we can reconstruct some pretty large chunks of the genome from the mate-pair ends. This directory contains the trim9.joins file, which is needed for doing the **homework** to attempt to reconstruct the genome.
   * euler
     * euler-assembly1/
@@ Line 30: / Line 30: @@
   * mira
     * mira-assembly1/
+  * velvet
-    * velvet-assembly2/ 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 1755 nodes and n50 of 41723, max {contig size} 142286, total {genome size} 2468925.
+      * 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-assembly3/ 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-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.
       * velveth_de out 21 -shortPaired /campusdata/BME235/data/Pog/solid_run/paired/output/doubleEncoded_input.de
       * velvetg_de out -exp_cov 50 -cov_cutoff 13 -ins_length 2200
       * Final graph has 3602 nodes and n50 of 4851, max 94854, total 1767903, using 28785664/61262410 reads
   * 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.
+    * 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.
@@ Line 56: / Line 57: @@
     * The output has 2664 contigs, comprising 443,648 bases (still less than the de novo assembly).
     * The longest contig is only 1876 bases.
+  * SOAPdenovo-assembly1/ First run of SOAPdenovo on illumina paired ends.
+    * SOAPdenovo requires fastq input files.
+    * It was used to assemble the Panda genome by BGI.
+    * Used kolossus which has 1TB and 64cpus.
+    * Ran with k=31 and k=23.  k=31 was better (9k maxcontig)
+    * so ran with filling -R to get 12k maxcontig.
+    * Then ran the scaffolding steps with 200bp insert size.
+    * For all steps, used low default cutoffs since our 10x coverage
+    * is not high.  21k max scaffold size.  Estimated
+    * genome size is around 3G.  The 4 steps are
+    * 1. pregraph (3.5 to 4.5 hours for 30 to 60 cpus)
+    * 2. contig (1.3 hours)
+    * 3. map (0.6 hours with 60cpus) - paired ends
+    * 4. scaff (1 hour with 60cpus)

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