 Christiane Hassenrueck
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0fee3cb568
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updated and validated metaG workflow until bin summary
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1 month ago |
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Christiane Hassenrueck
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34de416ea8
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updating workflow to latest program version and dependencies, pruning annotation option
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2 months ago |
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Christiane Hassenrueck
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e5304e013c
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Different content of repo modified in different locations
Merge branch 'master' of https://git.io-warnemuende.de/bio_inf/workflow_templates
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3 months ago |
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Christiane Hassenrueck
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3dae33f92e
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saving env exports for metaG pipeline state until March 2023
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3 months ago |
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Christiane Hassenrueck
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c4a24efac8
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bug fix organelle classification
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4 months ago |
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Christiane Hassenrueck
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73294983a6
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implemented user-configurable pool option for dada, bug fix SILVA taxonomy parsing
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4 months ago |
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Christiane Hassenrueck
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506c410927
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updated dbcan version, added annotation gene catalogue, optimization HLRN partitions, bug fix counting sequences
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4 months ago |
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Christiane Hassenrueck
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5635164b32
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updated bin postprocessing, removing InterProScan from default bin annotation summary, updating KEGG release
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5 months ago |
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Christiane Hassenrueck
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d61257d310
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improvement BAT, updated slurm config, bug fix reassembly to catch failed spades runs, adjust pdf height in final bin summary plot
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5 months ago |
chassenr
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3faaa16755
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Merge branch 'master' of https://git.io-warnemuende.de/bio_inf/workflow_templates
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6 months ago |
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chassenr
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9d98d4d2e8
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updated wmetaG workflow schematic
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6 months ago |
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Christiane Hassenrueck
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bd636236b9
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added parsing script for PCycDB output
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6 months ago |
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Christiane Hassenrueck
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2fbb176312
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fixing typos in binning rules
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6 months ago |
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Christiane Hassenrueck
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881fac4fa2
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added binspreader refinement to per sample binning
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6 months ago |
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Christiane Hassenrueck
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8bd91f68f9
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added contig count to bin summary, added gene catalogue classification
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7 months ago |
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Christiane Hassenrueck
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accfb4ab18
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modified counting sequences in raw data to accept bz2 and gz compressed input; bug fix in denoising script
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7 months ago |
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Christiane Hassenrueck
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f190c307f4
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included option in amplicon wf to combine denoised data with previously analyzed data set
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7 months ago |
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Christiane Hassenrueck
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3ab80d3633
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added SCycDB for bin annotations, updated annotation summary parsing code
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7 months ago |
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Christiane Hassenrueck
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33b2db7628
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implementation of more stringent filtering thresholds for bin and gene quantification based on bam files
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8 months ago |
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Christiane Hassenrueck
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bf08bcfac9
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bug fix in fixing incertae sedis taxa in amplicon workflow
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8 months ago |
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Christiane Hassenrueck
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8683498719
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bug fix in final bin summary parsing, added user-configurable flag for percentage identity in bin quantification, started gene catalogue quantification
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8 months ago |
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chassenr
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cb85a99763
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checkm2 integration in final bins parsing script
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8 months ago |
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Christiane Hassenrueck
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731a204bf3
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bug fixes in user-configurable completeness and contamination thresholds and bin reassembly
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8 months ago |
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Christiane Hassenrueck
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005fa92b02
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added completeness and contamination thresholds in metaWRAP bin refinement to config, started checkm2 integration in final bin assessment
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8 months ago |
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Christiane Hassenrueck
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d5ff248424
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updated citation for amplicon workflow
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8 months ago |
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Christiane Hassenrueck
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10e0d4f327
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bug fix amplicon wf in parsing blast output with only 1 qseqid
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9 months ago |
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Christiane Hassenrueck
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95d4f80c30
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bug fix in kraken summary (removing all euks now)
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9 months ago |
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Christiane Hassenrueck
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e5e66bce93
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started adding gene catalogue
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9 months ago |
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Christiane Hassenrueck
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04a2e60b85
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bug fix in reading BAT output in final_bins R script
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10 months ago |
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Christiane Hassenrueck
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db93f54dd8
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updated metaG workflow (running IOWseq000015)
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11 months ago |
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Christiane Hassenrueck
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7b8e42fe9b
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bug fix trimming amplicon mixed orientation
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11 months ago |
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Christiane Hassenrueck
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ecfcb15418
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cleaning of comments in amplicon classification rules
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12 months ago |
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chassenr
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77e0a9d1bf
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updated metaG workflow schematic
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12 months ago |
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chassenr
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5660e3700d
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updated amplicon workflow schematic
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1 year ago |
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chassenr
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f5ddab9a47
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updated amplicon workflow schematic
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1 year ago |
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Christiane Hassenrueck
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25064ece01
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adapted amplicon workflow for directed and mixed orientation libraries
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1 year ago |
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chassenr
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1aaaaf4975
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update amplicon workflow schematic
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1 year ago |
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Christiane Hassenrueck
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44ba02faaf
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validation of amplicon workflow for 18S
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1 year ago |
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Christiane Hassenrueck
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cea9c7734f
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amplicon workflow update validation 16S complete
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1 year ago |
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chassenr
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0b72c8c6e2
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draft for improved blast classification amplicon workflow
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1 year ago |
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Christiane Hassenrueck
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787a6f16a1
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bug fixing rescue unmerged completed
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1 year ago |
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chassenr
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d9df03414a
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added rescue unmerged option to amplicon workflow, testing
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1 year ago |
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chassenr
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2d4ad93b91
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merge commit
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1 year ago |
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chassenr
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b5389056c0
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updated annotation parsing and cleaned template for post-processing
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1 year ago |
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Christiane Hassenrueck
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6d373e46f8
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further revisions amplicon workflow (work in progress), minor updates metaG
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1 year ago |
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chassenr
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c9d5f5bd40
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added NCycDB to metaG, started updating maplicon workflow to include organelle 16S classification (work in progress)
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1 year ago |
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chassenr
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e375b73a5b
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added NCycDB to metaG, started updating maplicon workflow to include organelle 16S classification (work in progress)
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1 year ago |
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chassenr
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8c14883d9f
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updated licenses
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1 year ago |
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chassenr
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dfd1bfe575
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updated snakefile
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1 year ago |
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chassenr
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9be544a1ae
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cleaning up repo
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1 year ago |
