| 4f57b57 | Shaun Jackman | 04 August 2017, 18:53:50 UTC | abyss2/Makefile: Change N to 9 ABySS 2.0 was run with N=7 mp=mp6k.in ABySS 2.0 + Sealer was run with N=9 mp=mp6k+unknown.in | 04 August 2017, 18:53:50 UTC |
| 074c7c5 | Shaun Jackman | 31 July 2017, 19:00:23 UTC | Makefile: Add abyss2 | 31 July 2017, 19:00:23 UTC |
| 83db99a | Shaun Jackman | 31 July 2017, 18:48:19 UTC | Add abyss2/pe400.in and abyss/2mp6k+unknown.in | 31 July 2017, 18:49:20 UTC |
| b87d460 | Shaun Jackman | 31 July 2017, 18:48:09 UTC | Add abyss2/bin/run-abyss-bloom-dbg | 31 July 2017, 18:49:19 UTC |
| 222d8fa | Shaun Jackman | 31 July 2017, 18:47:52 UTC | Add abyss2/Makefile | 31 July 2017, 18:49:19 UTC |
| 83d0232 | Shaun Jackman | 09 December 2016, 00:38:12 UTC | Add a link to the assemblies archive on NCBI | 09 December 2016, 00:38:12 UTC |
| e0b447c | Shaun Jackman | 09 December 2016, 00:24:39 UTC | Update README.md | 09 December 2016, 00:27:04 UTC |
| 1be8623 | Shaun Jackman | 29 November 2016, 00:09:07 UTC | Decrease MAX_MEM_GB from 2500 to 750 | 29 November 2016, 00:09:07 UTC |
| 6083d27 | Shaun Jackman | 25 November 2016, 18:52:39 UTC | Map the reads to the assembly and store the CIGAR | 25 November 2016, 18:52:39 UTC |
| 7f48b4d | Shaun Jackman | 25 November 2016, 18:51:42 UTC | Add soapdenovo/raw/Makefile and hsapiens.config | 25 November 2016, 18:51:42 UTC |
| 269c4e5 | Shaun Jackman | 24 November 2016, 18:08:05 UTC | Analayze the assemblies using QUAST | 24 November 2016, 18:08:05 UTC |
| 8bde873 | Shaun Jackman | 18 November 2016, 22:22:55 UTC | Regenerate metrics.tsv | 18 November 2016, 22:22:55 UTC |
| 4161905 | Shaun Jackman | 18 November 2016, 22:22:26 UTC | Calculate genome coverage and sequence identity | 18 November 2016, 22:22:26 UTC |
| fc91b65 | Shaun Jackman | 16 November 2016, 19:37:44 UTC | sga: Add assemblies of uncorrected and corrected | 16 November 2016, 19:37:44 UTC |
| 01fec6c | Shaun Jackman | 16 November 2016, 19:28:45 UTC | Interleave uncorrected paired-end reads | 16 November 2016, 19:29:45 UTC |
| cc7efc6 | Shaun Jackman | 03 November 2016, 22:08:24 UTC | sga: Use sga fm-merge to reduce memory usage | 03 November 2016, 22:08:32 UTC |
| 65bd9b7 | Shaun Jackman | 02 November 2016, 22:58:31 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Update sga | 02 November 2016, 22:59:19 UTC |
| 9bf90c8 | Shaun Jackman | 02 November 2016, 22:57:23 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Update discovardenovo/links discovardenovo/links/bionano | 02 November 2016, 22:59:00 UTC |
| 84ef1e6 | Shaun Jackman | 02 November 2016, 22:52:59 UTC | Add contig stats | 02 November 2016, 22:52:59 UTC |
| d8d0613 | Shaun Jackman | 02 November 2016, 22:51:44 UTC | Add SGA scaffolds and scaftigs | 02 November 2016, 22:51:44 UTC |
| 8d20976 | Shaun Jackman | 02 November 2016, 22:51:09 UTC | Hardcode the paths to ABySS executables | 02 November 2016, 22:51:09 UTC |
| c3abdc4 | Shaun Jackman | 02 November 2016, 22:49:21 UTC | soapdenovo: Create hsapiens-contigs.fa | 02 November 2016, 22:49:21 UTC |
| 0424aea | Shaun Jackman | 02 November 2016, 22:48:16 UTC | sga: Create scaffolds.fa using MergeContigs sga scaffold2fasta blows an assertion. See https://github.com/jts/sga/issues/125 | 02 November 2016, 22:49:10 UTC |
| 6e83dec | Shaun Jackman | 02 November 2016, 22:47:16 UTC | Add bin/sga-scaf-to-path | 02 November 2016, 22:47:16 UTC |
| 9f08149 | Shaun Jackman | 08 August 2016, 16:02:32 UTC | Rename pe600.realpath to pe400.realpath | 08 August 2016, 16:02:32 UTC |
| f19597f | Shaun Jackman | 05 August 2016, 19:11:34 UTC | bcalm: Change bglue -nb-cores to 12 See https://github.com/GATB/bcalm/issues/10 | 05 August 2016, 19:11:34 UTC |
| b7f6356 | Shaun Jackman | 05 August 2016, 19:11:17 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Add soapdenovo/k79 | 05 August 2016, 19:11:17 UTC |
| c704e9a | Shaun Jackman | 05 August 2016, 19:05:45 UTC | Add soapdenovo/k79 | 05 August 2016, 19:10:40 UTC |
| 0c1c2f0 | Shaun Jackman | 04 August 2016, 23:07:33 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Add soapdenovo/k95 and soapdenovo/k111 | 04 August 2016, 23:07:33 UTC |
| fc0783c | Shaun Jackman | 04 August 2016, 23:06:32 UTC | Add soapdenovo/k95 and soapdenovo/k111 | 04 August 2016, 23:06:32 UTC |
| 90e7766 | Shaun Jackman | 02 August 2016, 23:00:21 UTC | assembly-stats.rmd: Add abyss/k144/sealer | 02 August 2016, 23:00:21 UTC |
| adf2027 | Shaun Jackman | 02 August 2016, 22:52:18 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Use abyss/k144 rather than abyss | 02 August 2016, 22:52:18 UTC |
| c35cdfc | Shaun Jackman | 02 August 2016, 22:27:50 UTC | Use abyss/k144 rather than abyss | 02 August 2016, 22:27:50 UTC |
| 37028a7 | Shaun Jackman | 02 August 2016, 18:34:24 UTC | assembly-stats.rmd: Add contig sealer results | 02 August 2016, 18:34:24 UTC |
| ef36677 | Shaun Jackman | 02 August 2016, 18:33:34 UTC | assembly-stats.rmd: Add ABySS 2.0 | 02 August 2016, 18:33:34 UTC |
| 686c695 | Shaun Jackman | 02 August 2016, 18:20:32 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Add ABySS 2.0 abyss2/k144 abyss2/k144/sealer abyss2/k144/bionano abyss2/k144/sealer/bionano | 02 August 2016, 18:20:59 UTC |
| db1e1ae | Shaun Jackman | 02 August 2016, 16:58:42 UTC | Add ABySS 2.0 abyss2/k144 abyss2/k144/sealer abyss2/k144/bionano abyss2/k144/sealer/bionano | 02 August 2016, 17:03:03 UTC |
| 12613ba | Shaun Jackman | 31 July 2016, 17:23:04 UTC | assembly-stats.rmd: Add abyss/k144/bionano Add abyss/k144/bionano abyss/k144/sealer/bionano | 31 July 2016, 17:23:04 UTC |
| e3b5850 | Shaun Jackman | 31 July 2016, 17:15:14 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Add abyss/k144/bionano abyss/k144/sealer/bionano | 31 July 2016, 17:15:14 UTC |
| d4bf666 | Shaun Jackman | 31 July 2016, 17:14:28 UTC | Add abyss/k144/bionano abyss/k144/sealer/bionano Results are different than bionano/aggressive-B2-N2. | 31 July 2016, 17:14:28 UTC |
| a7eab78 | Shaun Jackman | 30 July 2016, 05:25:34 UTC | assembly-stats.rmd: Plot contig metrics | 30 July 2016, 05:37:43 UTC |
| aab5ae9 | Shaun Jackman | 30 July 2016, 05:01:39 UTC | assembly-stats.rmd: Fix white space | 30 July 2016, 05:01:39 UTC |
| 5deaaee | Shaun Jackman | 30 July 2016, 04:57:21 UTC | assembly-stats.rmd: Adjust labels | 30 July 2016, 04:57:21 UTC |
| a464bda | Shaun Jackman | 30 July 2016, 04:56:02 UTC | assembly-stats.rmd: Remove version numbers | 30 July 2016, 04:57:13 UTC |
| 408e2f8 | Shaun Jackman | 30 July 2016, 04:45:06 UTC | assembly-stats.rmd: Plot NG50 and NGA50 | 30 July 2016, 04:45:06 UTC |
| 8121c31 | Shaun Jackman | 30 July 2016, 01:36:05 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Use bionano/aggressive-B2-N2 | 30 July 2016, 01:36:05 UTC |
| 58f6eb1 | Shaun Jackman | 30 July 2016, 01:35:45 UTC | Use bionano/aggressive-B2-N2 | 30 July 2016, 01:35:45 UTC |
| c5f0ef5 | Shaun Jackman | 30 July 2016, 00:13:32 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Add ABySS + BioNano | 30 July 2016, 00:13:32 UTC |
| 6bc5c77 | Shaun Jackman | 30 July 2016, 00:12:57 UTC | Add ABySS + BioNano | 30 July 2016, 00:12:57 UTC |
| 94efe2b | Shaun Jackman | 30 July 2016, 00:02:41 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Add discovardenovo/abyss-scaffold/bionano | 30 July 2016, 00:02:41 UTC |
| c8968ac | Shaun Jackman | 29 July 2016, 21:59:45 UTC | Add discovardenovo/abyss-scaffold/bionano | 29 July 2016, 21:59:45 UTC |
| 98638ea | Shaun Jackman | 29 July 2016, 21:57:06 UTC | time hybridScaffold.pl and bwa mem | 29 July 2016, 21:57:06 UTC |
| 9457156 | Shaun Jackman | 29 July 2016, 21:53:34 UTC | assembly-stats.rmd: Install rmarkdown | 29 July 2016, 21:53:34 UTC |
| 8424ec1 | Shaun Jackman | 29 July 2016, 21:52:06 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Add BioNano scaffolding | 29 July 2016, 21:52:06 UTC |
| 2d09621 | Shaun Jackman | 29 July 2016, 21:51:49 UTC | Add BioNano scaffolding | 29 July 2016, 21:51:49 UTC |
| baa9e82 | Shaun Jackman | 29 July 2016, 21:38:54 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Add DISCOVARdenovo scaffolding | 29 July 2016, 21:38:54 UTC |
| a9b2fe1 | Shaun Jackman | 29 July 2016, 21:38:01 UTC | Add DISCOVARdenovo scaffolding | 29 July 2016, 21:38:25 UTC |
| 4a8613c | Shaun Jackman | 29 July 2016, 19:56:07 UTC | Change the number of threads from 32 to 64 | 29 July 2016, 19:56:07 UTC |
| 3b78d94 | Shaun Jackman | 29 July 2016, 19:46:44 UTC | Remove quast | 29 July 2016, 19:46:44 UTC |
| b9afaf3 | Shaun Jackman | 29 July 2016, 19:41:31 UTC | discovardenovo: Rename BESST to besst | 29 July 2016, 19:41:31 UTC |
| 87c200d | Shaun Jackman | 29 July 2016, 19:38:49 UTC | soapdenovo: Symlink hsapiens-scaffolds.fa Increase threads to 64. Remove genome size, since NG50 was calculated incorrectly. | 29 July 2016, 19:38:49 UTC |
| 0351bb1 | Shaun Jackman | 29 July 2016, 19:36:51 UTC | sga: Add scaffolding | 29 July 2016, 19:36:51 UTC |
| 4866181 | Shaun Jackman | 29 July 2016, 19:33:50 UTC | Revise assembly-stats.rmd for non-ABySS assemblies | 29 July 2016, 19:33:50 UTC |
| 24f942c | Shaun Jackman | 29 July 2016, 18:58:52 UTC | Regenerate assembly-stats.tsv samtobreak.tsv Use Sealer results k144/abyss-sealed-scaffolds.fa | 29 July 2016, 18:58:52 UTC |
| b62acb5 | Shaun Jackman | 29 July 2016, 18:57:59 UTC | discovardenovo: Add abyss-scaffold | 29 July 2016, 18:57:59 UTC |
| 6e1a1c0 | Shaun Jackman | 27 July 2016, 20:47:46 UTC | abyss: Symlink k144/abyss-sealed-scaffolds.fa | 29 July 2016, 18:57:08 UTC |
| a175bb4 | Shaun Jackman | 27 July 2016, 20:47:20 UTC | Add abyss-samtobreak.tsv abyss-stats.tsv | 27 July 2016, 20:47:20 UTC |
| 6724394 | Shaun Jackman | 27 July 2016, 20:47:06 UTC | Add abyss-stats.rmd | 27 July 2016, 20:47:06 UTC |
| 8686af3 | Shaun Jackman | 27 July 2016, 19:34:02 UTC | Add assembly-stats.tsv and samtobreak.tsv | 27 July 2016, 19:57:39 UTC |
| de3a2dd | Shaun Jackman | 27 July 2016, 19:33:44 UTC | Update bin/abyss-samtobreak-to-tsv | 27 July 2016, 19:54:08 UTC |
| c9d15e4 | Shaun Jackman | 27 July 2016, 17:53:34 UTC | Add BCALM | 27 July 2016, 17:53:34 UTC |
| 307cc48 | Shaun Jackman | 27 July 2016, 17:49:12 UTC | Add DISCOVARdenovo | 27 July 2016, 17:49:12 UTC |
| 8a6b757 | Shaun Jackman | 27 July 2016, 17:31:53 UTC | Add SOAPdenovo | 27 July 2016, 17:31:53 UTC |
| 07fe1f9 | Shaun Jackman | 25 July 2016, 18:59:58 UTC | Makefile: Add SGA | 25 July 2016, 18:59:58 UTC |
| 3c2208d | Shaun Jackman | 23 July 2016, 00:19:02 UTC | Add bionano config files | 23 July 2016, 00:20:20 UTC |
| dff81ef | Shaun Jackman | 22 July 2016, 22:22:37 UTC | Add sga | 22 July 2016, 22:22:56 UTC |
| 02e4508 | Shaun Jackman | 22 July 2016, 21:47:33 UTC | Add versions.tsv | 22 July 2016, 21:54:03 UTC |
| 67eab4b | Shaun Jackman | 22 July 2016, 21:42:46 UTC | Add dependencies | 22 July 2016, 21:54:02 UTC |
| deee413 | Shaun Jackman | 22 July 2016, 21:39:24 UTC | Add samtobreak.tsv | 22 July 2016, 21:39:24 UTC |
| 1cb2261 | Shaun Jackman | 22 July 2016, 21:36:09 UTC | Add soapdenovo | 22 July 2016, 21:36:09 UTC |
| c781f4f | Shaun Jackman | 22 July 2016, 21:30:21 UTC | Add masurca | 22 July 2016, 21:31:47 UTC |
| 9b1aab5 | Shaun Jackman | 22 July 2016, 21:28:02 UTC | Add allpaths-lg | 22 July 2016, 21:28:02 UTC |
| b297c68 | Shaun Jackman | 22 July 2016, 21:19:28 UTC | bin/qsub-make: Increase threads and memory | 22 July 2016, 21:19:28 UTC |
| 0120f8c | Shaun Jackman | 22 July 2016, 21:18:31 UTC | abyss: Set TMPDIR | 22 July 2016, 21:18:31 UTC |
| 48c8666 | Shaun Jackman | 21 July 2016, 23:11:17 UTC | Add bcalm/Makefile | 21 July 2016, 23:11:17 UTC |
| f5e47e6 | Shaun Jackman | 21 July 2016, 00:41:49 UTC | abyss: Run ABySS on a single machine to compare | 21 July 2016, 00:41:49 UTC |
| 47bb0dc | Shaun Jackman | 21 July 2016, 00:07:12 UTC | Add discovardenovo/Makefile | 21 July 2016, 00:07:12 UTC |
| b910ef0 | Shaun Jackman | 20 July 2016, 23:51:25 UTC | abyss: Use every 16th value of k with sealer | 20 July 2016, 23:51:25 UTC |
| f8a509c | Shaun Jackman | 19 July 2016, 21:28:34 UTC | Add BioNano Genomics HybridScaffold | 19 July 2016, 21:28:34 UTC |
| 139bc73 | Shaun Jackman | 19 July 2016, 21:28:11 UTC | Increase number of threads from 8 to 32 | 19 July 2016, 21:28:11 UTC |
| 82c0a4d | Shaun Jackman | 05 July 2016, 01:37:38 UTC | bionano/Makefile: Close gaps using abyss-sealer | 05 July 2016, 01:41:37 UTC |
| 7c9ca38 | Shaun Jackman | 05 July 2016, 01:35:23 UTC | Calculate assembly metrics using abyss-samtobreak | 05 July 2016, 01:35:23 UTC |
| 5b8beb4 | Shaun Jackman | 05 July 2016, 01:34:48 UTC | Use reference genome from /projects/btl | 05 July 2016, 01:35:04 UTC |
| 322dc32 | Shaun Jackman | 28 June 2016, 23:49:55 UTC | bionano/samtobreak.tsv: Add Total_breakpoints | 28 June 2016, 23:49:55 UTC |
| a343689 | Shaun Jackman | 28 June 2016, 23:49:28 UTC | Regenerate bionano/samtobreak.tsv: Add -B2 -N2 | 28 June 2016, 23:49:28 UTC |
| 4d10627 | Shaun Jackman | 28 June 2016, 23:25:41 UTC | Regenerate bionano/stats.tsv: Add -B2 -N2 | 28 June 2016, 23:41:37 UTC |
| 78e7fc3 | Shaun Jackman | 28 June 2016, 23:25:18 UTC | bionano/Makefile: Add -B2 -N2 | 28 June 2016, 23:41:37 UTC |
| 52ed0f8 | Shaun Jackman | 24 June 2016, 22:49:45 UTC | bionano: Add AJmother_autoNoise1.err | 28 June 2016, 23:41:37 UTC |
| 72b3b33 | Shaun Jackman | 24 June 2016, 22:49:24 UTC | bionano: Add samtobreak.tsv stats.tsv | 28 June 2016, 23:41:36 UTC |
| 8537e6c | Shaun Jackman | 24 June 2016, 22:46:30 UTC | bionano: Add Makefile | 24 June 2016, 22:49:05 UTC |
