| c99080d | Ino de Bruijn | 25 October 2014, 10:19:17 UTC | Add Kraken validation. Untested. | 25 October 2014, 10:19:17 UTC |
| 87728cc | Ino de Bruijn | 26 July 2014, 09:03:52 UTC | Multithreading for newbler | 26 July 2014, 09:03:52 UTC |
| 40304c7 | Ino de Bruijn | 24 July 2014, 16:04:13 UTC | Add separate mapping rule | 24 July 2014, 16:04:13 UTC |
| d452c88 | Ino de Bruijn | 21 July 2014, 14:43:41 UTC | Merge branch 'master' of https://github.com/inodb/metassemble | 21 July 2014, 14:43:41 UTC |
| da85ea8 | Ino de Bruijn | 21 July 2014, 14:43:19 UTC | Add case when no coverage for genome in bed histogram | 21 July 2014, 14:43:19 UTC |
| 246134d | Ino de Bruijn | 19 June 2014, 18:59:18 UTC | Fix percentage_covered error when contig has no reads mapping | 19 June 2014, 18:59:18 UTC |
| a9eca38 | Ino de Bruijn | 22 May 2014, 14:30:14 UTC | fix percentage covered 0% bug | 22 May 2014, 14:30:14 UTC |
| a5b3abc | Ino de Bruijn | 15 May 2014, 08:39:39 UTC | Add GC and percentage coverage | 15 May 2014, 08:39:39 UTC |
| 6b7b06c | Ino de Bruijn | 30 April 2014, 15:27:29 UTC | Default parameters were not reflecting doc parameters | 30 April 2014, 15:27:29 UTC |
| 5d3e270 | Ino de Bruijn | 25 April 2014, 09:32:21 UTC | Update usage | 25 April 2014, 09:32:21 UTC |
| fe8070d | Ino de Bruijn | 25 April 2014, 09:26:33 UTC | Update documentation | 25 April 2014, 09:26:33 UTC |
| 96e8f8c | Ino de Bruijn | 24 April 2014, 12:10:25 UTC | Add CONCOCT script to compute coverage of contigs from bam file instead of using awk. Fixes contigs not appearing in output coverage.percontig if coverage is zero. Change java memory usage to parameter. | 24 April 2014, 12:10:25 UTC |
| de219bf | Ino de Bruijn | 24 April 2014, 07:49:04 UTC | Fixes validation | 24 April 2014, 07:49:04 UTC |
| 00847b9 | Ino de Bruijn | 17 March 2014, 12:25:08 UTC | Add reference validation with broken up contigs. | 17 March 2014, 12:25:08 UTC |
| 69f0ec1 | Ino de Bruijn | 21 January 2014, 09:44:03 UTC | Merge branch 'master' of https://github.com/inodb/metassemble | 21 January 2014, 09:44:03 UTC |
| ae77a7a | Ino de Bruijn | 21 January 2014, 09:43:36 UTC | Add process substitution arguments for map-bowtie2-markduplicates | 21 January 2014, 09:43:36 UTC |
| 599d68e | Ino de Bruijn | 02 December 2013, 10:37:25 UTC | Fix wrong merge | 02 December 2013, 10:37:25 UTC |
| 4f2944c | Ino de Bruijn | 02 December 2013, 10:36:09 UTC | Merge | 02 December 2013, 10:36:09 UTC |
| ce555e2 | Ino de Bruijn | 02 December 2013, 10:34:23 UTC | Remove default checkpointing for Ray. Add qsub test | 02 December 2013, 10:34:23 UTC |
| c03ed0d | Ino de Bruijn | 27 November 2013, 15:33:56 UTC | Use METASSEMBLE_DIR variable instead of SCRIPTDIR | 27 November 2013, 15:33:56 UTC |
| 8ee60cb | Ino de Bruijn | 26 September 2013, 19:53:41 UTC | Change java heap and perm space for MarkDuplicates. | 26 September 2013, 19:53:41 UTC |
| ec6c57e | Ino de Bruijn | 08 August 2013, 11:00:38 UTC | Add extra bowtie2 options. Changes incorrect bowtie2 calling. (tested) | 08 August 2013, 11:02:24 UTC |
| f59e6e1 | Ino de Bruijn | 07 August 2013, 16:05:55 UTC | Adds small changes. Easier to delete results. Adds bowtie2 validation mapping (untested). | 07 August 2013, 16:05:55 UTC |
| faa6951 | Ino de Bruijn | 07 August 2013, 16:00:38 UTC | Change insert metrics parsing for bambus2 | 07 August 2013, 16:00:38 UTC |
| 70b29e0 | Ino de Bruijn | 18 June 2013, 13:03:13 UTC | Merge branch 'master' of https://github.com/inodb/metassemble | 18 June 2013, 13:03:13 UTC |
| 4a7da10 | Ino de Bruijn | 18 June 2013, 13:00:18 UTC | Adds validation (untested). Adds bwa mem mapping. | 18 June 2013, 13:00:18 UTC |
| bcdd067 | inodb | 16 April 2013, 08:09:39 UTC | Update README.md Added METASSEMBLE_DIR environment variable to the installation instructions. | 16 April 2013, 08:09:39 UTC |
| de05cae | Ino de Bruijn | 08 April 2013, 07:58:03 UTC | Merge branch 'master' of github.com:inodb/metassemble | 08 April 2013, 07:58:03 UTC |
| 9b66eaf | Ino de Bruijn | 08 April 2013, 07:57:29 UTC | Removed cluster specific module load commands | 08 April 2013, 07:57:29 UTC |
| cb91e4d | Ino de Bruijn | 05 April 2013, 20:01:55 UTC | Umer found bug. Changed SCRIPTDIR name. Partially tested make test, but couldn't do the entire thing due to UPPMAX being partially down. | 05 April 2013, 20:01:55 UTC |
| d74e551 | Ino de Bruijn | 08 March 2013, 17:32:31 UTC | Update README.md | 08 March 2013, 17:32:31 UTC |
| 53a4250 | Ino de Bruijn | 08 March 2013, 17:27:29 UTC | Change the example | 08 March 2013, 17:27:29 UTC |
| 72c638f | Ino de Bruijn | 08 March 2013, 17:10:05 UTC | Restructure metassemle and tests for qsub | 08 March 2013, 17:10:05 UTC |
| 8a40518 | Ino de Bruijn | 07 March 2013, 09:45:44 UTC | Merge branch 'master' of github.com:inodb/metassemble | 07 March 2013, 09:45:44 UTC |
| ea15133 | inodb | 07 March 2013, 09:42:58 UTC | Update README.md | 07 March 2013, 09:42:58 UTC |
| e380ee7 | inodb | 07 March 2013, 09:42:27 UTC | Update README.md with gnu-make-job-scheduler | 07 March 2013, 09:42:27 UTC |
| d58dca1 | Ino de Bruijn | 07 March 2013, 09:39:21 UTC | Remove sbatch_job | 07 March 2013, 09:39:21 UTC |
| fbd3aac | Ino de Bruijn | 05 March 2013, 14:49:48 UTC | Update gnu-make-job-scheduler library | 07 March 2013, 09:35:07 UTC |
| 7d48e93 | Ino de Bruijn | 06 March 2013, 09:23:40 UTC | Chang mpiexec of ray to a parameter (for aprun) | 06 March 2013, 09:23:40 UTC |
| cd1b82d | Ino de Bruijn | 05 March 2013, 14:50:15 UTC | Merge branch 'master' of github.com:inodb/metassemble | 05 March 2013, 14:50:15 UTC |
| b0536da | Ino de Bruijn | 05 March 2013, 14:49:48 UTC | Change sbatch_job from symbolic link to actual script | 05 March 2013, 14:49:48 UTC |
| 9116065 | Ino de Bruijn | 05 March 2013, 14:36:49 UTC | Merge branch 'master' of github.com:inodb/metassemble | 05 March 2013, 14:36:49 UTC |
| 61cf1e5 | Ino de Bruijn | 05 March 2013, 14:31:13 UTC | Add quality trim skip + some minor changes. | 05 March 2013, 14:31:13 UTC |
| 283c862 | Ino de Bruijn | 05 March 2013, 14:03:32 UTC | Support older versions of bash. Lindgren did not have support for {1..4..2} type syntax for determining directory names. Now seq is used to determine the k values. | 05 March 2013, 14:03:32 UTC |
| 22a8064 | Ino de Bruijn | 26 February 2013, 18:58:52 UTC | Formats README | 26 February 2013, 18:58:52 UTC |
| 68bce21 | Ino de Bruijn | 26 February 2013, 18:56:37 UTC | Add Usage to Readme. Change extension to md. | 26 February 2013, 18:56:37 UTC |
| 3316cdd | Ino de Bruijn | 26 February 2013, 18:40:12 UTC | Add HMP test, update README. The HMP test downloads a test library and runs the pipeline with make test. It is now possible to check all dependencies. Also the jars from Picard have been added. | 26 February 2013, 18:46:24 UTC |
| f1ac36b | Ino de Bruijn | 26 February 2013, 09:25:29 UTC | Solve Ray Scaffold remake | 26 February 2013, 09:25:29 UTC |
| ebb0781 | Ino de Bruijn | 25 February 2013, 18:47:41 UTC | Add gnu-make-sbatch-tools as lib and bin. | 25 February 2013, 18:47:41 UTC |
| e056fca | Ino de Bruijn | 20 February 2013, 10:42:00 UTC | Break up Makefile in sbatch-less and with sbatch. Include dependency test. The sbatch parameters within the Makefile were not necessary for users without sbatch. Therefore a separate Makefile-sbatch was created that calls the Makefile. It comes from my other repository gnu-make-sbatch-tools. This commit also creates a dependecy checker script to make sure all dependencies are met to be able to run the pipeline. | 20 February 2013, 10:42:00 UTC |
| 9ff17e1 | Ino de Bruijn | 15 February 2013, 15:11:08 UTC | Add Ray to Makefile-validate-assemblies Add Ray to validation. Both contigs and scaffolding. Remove old validation script rules. | 15 February 2013, 15:11:08 UTC |
| c1db172 | Ino de Bruijn | 12 February 2013, 16:42:32 UTC | OK, so that was why I shouldn't change the extension to md. Formatting gets all craaaazy. I should read up on markdown. | 12 February 2013, 16:42:32 UTC |
| 0755c92 | Ino de Bruijn | 12 February 2013, 16:39:08 UTC | Changed extension to md so github will recognize it as markdown. | 12 February 2013, 16:39:08 UTC |
| e041799 | Ino de Bruijn | 05 February 2013, 16:46:36 UTC | Small changes, scaffold dir for ray | 05 February 2013, 16:46:36 UTC |
| 890904a | Ino de Bruijn | 01 February 2013, 12:46:27 UTC | Added Ray | 01 February 2013, 12:46:27 UTC |
| fc0fd02 | Ino de Bruijn | 24 January 2013, 09:17:42 UTC | README file had wrong quality trimming script name. | 24 January 2013, 09:17:42 UTC |
| f98254f | Ino de Bruijn | 24 January 2013, 09:14:35 UTC | README file had wrong quality trimming script name. | 24 January 2013, 09:14:35 UTC |
| 41a6ba4 | Ino de Bruijn | 24 January 2013, 09:11:48 UTC | scripts/Makefile Changed deprecated quality trimming script to scickle (does the same window trimming). scripts/makefile-examples/ Added some other Makefile examples if one prefers to perform a specific assembly. scripts/validate/map-bwa-markduplicates.sh Mapping with bwa now allows one to set the alignment parameters as well. | 24 January 2013, 09:11:48 UTC |
| 85d4629 | Ino de Bruijn | 10 January 2013, 16:21:53 UTC | Added some Makefile examples. | 10 January 2013, 16:21:53 UTC |
| 673abdf | Ino de Bruijn | 14 November 2012, 23:21:43 UTC | Changed file size test | 14 November 2012, 23:21:43 UTC |
| 207a2b8 | Ino de Bruijn | 06 November 2012, 23:31:10 UTC | Python implementation to calculate purity. | 06 November 2012, 23:31:10 UTC |
| 941a08c | Ino de Bruijn | 06 November 2012, 11:46:05 UTC | Merge branch 'master' of https://github.com/inodb/metassemble Conflicts: README | 06 November 2012, 11:46:05 UTC |
| 402438c | Ino de Bruijn | 06 November 2012, 11:37:23 UTC | Updated README file, changed Bambus2.done to linear scaffolds so it can be made in the similar way as the other assemblies by providing its path on the command line. | 06 November 2012, 11:41:12 UTC |
| fd84a13 | Ino de Bruijn | 06 November 2012, 11:37:23 UTC | Updated README file, changed Bambus2.done to linear scaffolds so it can be made in the similar way as the other assemblies by providing its path on the command line. | 06 November 2012, 11:37:23 UTC |
| 906a53e | Ino de Bruijn | 05 November 2012, 16:18:15 UTC | Merge branch 'experimental' of https://github.com/inodb/metassemble into experimental | 05 November 2012, 16:18:15 UTC |
| 9ada62e | Ino de Bruijn | 05 November 2012, 15:02:29 UTC | Commit used for half time report. | 05 November 2012, 16:11:20 UTC |
| 54db13f | Ino de Bruijn | 05 November 2012, 15:02:29 UTC | Commit used for half time report. | 05 November 2012, 15:02:29 UTC |
| 6c162ec | Ino de Bruijn | 08 October 2012, 13:04:20 UTC | Updated directory structure doc accordingly | 08 October 2012, 13:04:20 UTC |
| 35d7cff | Ino de Bruijn | 08 October 2012, 12:43:46 UTC | Added bambus2 scaffolding to the pipeline. Changed purity script to skip N's when calculating purity. | 08 October 2012, 12:43:46 UTC |
| e2b8e40 | Ino de Bruijn | 25 September 2012, 12:24:30 UTC | Most important fix was the incorrect folder copying of velveth output in Makefile. Velvet rule and Metavelvet rule were both wrong, fortunately didn't perform any assemblies with that rule yet. Problem lies in that it is difficult/impossible to specify multiple output files for one rule (http://www.cmcrossroads.com/cm-basics/12905-rules-with-multiple-outputs-in-gnu-make). | 25 September 2012, 12:24:30 UTC |
| 430a918 | Ino de Bruijn | 21 September 2012, 14:41:16 UTC | Updated directory structure doc with validation | 21 September 2012, 14:41:59 UTC |
| d511804 | Ino de Bruijn | 21 September 2012, 14:11:07 UTC | Stupid small mistake with not outputting delta-filter -g to the corresponding gcoords file. I wanted to use the original coords file anyway so it doesn't matter for the currently generated results. Actually it is better than if I would have used the correct gcoords file, since I wanted to know to how many other genomes each contig mapped in the pergenome-perassembly script. Of course if one wants to look at the best aligning results, the gcoords file should be used. | 21 September 2012, 14:11:07 UTC |
| 537b7cd | Ino de Bruijn | 21 September 2012, 09:49:18 UTC | Added Makefiles to replace the pipeline. Works a lot easier with keeping track of what files in the pipeline changed and sharing of the commands to create an assembly is easier. | 21 September 2012, 09:49:18 UTC |
| 5481e27 | Ino de Bruijn | 12 September 2012, 13:28:37 UTC | $'s were still escaped from sbatch commands in run-velvet. Should make better test suits for these things. | 12 September 2012, 13:29:00 UTC |
| dfd871e | Ino de Bruijn | 11 September 2012, 21:26:57 UTC | Getting the absolute path of the output dir was incorrect. | 11 September 2012, 21:26:57 UTC |
| 33aa639 | Ino de Bruijn | 11 September 2012, 12:35:15 UTC | is_in_array function still used integers, while 2.1 is a step now as well. | 11 September 2012, 12:35:15 UTC |
| 18e00d3 | Ino de Bruijn | 11 September 2012, 10:40:39 UTC | Directories and names restructured. ma-pipeline-all.sh now works in steps so you can schedule certain steps separately using sbatch or some other job scheduler. The new sbatch wrapper ma-pipeline-all-sbatch-wrapper.sh works but it could be that the 2.1/2.2 steps for velvet in ma-pipeline-all.sh and the metavelvet step cause some errors, because I haven't tested it with the sbatch inline commands removed. | 11 September 2012, 10:42:53 UTC |
| 2e8b911 | Ino de Bruijn | 23 July 2012, 20:17:20 UTC | Added a script that maps an assembly back to the reference using nucmer and then checks the metagenomic statistics using R. | 23 July 2012, 20:17:20 UTC |
| e13789f | Ino de Bruijn | 23 July 2012, 13:41:09 UTC | Added a script for looking at some metagenomic related stats after mapping the contigs with nucmer. Should also create a script that first runs nucmer with proper parameters such as allowing multiple alignment positions and then run the stats script. | 23 July 2012, 13:41:09 UTC |
| 9d4587d | Ino de Bruijn | 11 July 2012, 16:04:12 UTC | Gave the rename script some option handling. Apparently minimus2 outputs merged sequences as well with numbers starting from 1 so the input fastafile should not contain only numbers as accessions. | 11 July 2012, 16:04:12 UTC |
| bfec2a3 | Ino de Bruijn | 10 July 2012, 17:35:39 UTC | Spelling in the README. | 10 July 2012, 17:35:39 UTC |
| 6c484ae | Ino de Bruijn | 10 July 2012, 17:32:49 UTC | Added an R script for plotting different contig length histograms in one plot. Known bug when a cut-off is specified and 0 contigs above that length are found in one of the given contig files. | 10 July 2012, 17:32:49 UTC |
| 50e49ba | Ino de Bruijn | 06 July 2012, 16:30:20 UTC | Added metavelvet and idba. | 06 July 2012, 16:30:20 UTC |
| 290d5b9 | Ino de Bruijn | 06 July 2012, 11:51:15 UTC | First commit. Quality filters reads, velvet assembly over multiple kmers, minimus2 merging of velvet assemblies. | 06 July 2012, 11:51:15 UTC |
