output/quast/Lactococcus/report.tsv Version 1
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
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output/quast/Lactococcus/report.tsv
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Assembly spades # contigs (>= 0 bp) 245 # contigs (>= 1000 bp) 139 # contigs (>= 5000 bp) 60 # contigs (>= 10000 bp) 38 # contigs (>= 25000 bp) 27 # contigs (>= 50000 bp) 13 Total length (>= 0 bp) 2541749 Total length (>= 1000 bp) 2482734 Total length (>= 5000 bp) 2317176 Total length (>= 10000 bp) 2162610 Total length (>= 25000 bp) 1981093 Total length (>= 50000 bp) 1476297 # contigs 242 Largest contig 256070 Total length 2541371 GC (%) 34.97 N50 69806 N75 27770 L50 10 L75 25 # total reads 182073123 # left 91023201 # right 91023201 Mapped (%) 99.69 Properly paired (%) 98.29 Avg. coverage depth 10684 Coverage >= 1x (%) 100.0 # N's per 100 kbp 0.00 Complete BUSCO (%) 97.30 Partial BUSCO (%) 0.00 # predicted genes (unique) 952 # predicted genes (>= 0 bp) 949 + 3 part # predicted genes (>= 300 bp) 900 + 3 part # predicted genes (>= 1500 bp) 346 + 0 part # predicted genes (>= 3000 bp) 88 + 0 part # predicted rRNA genes 7 + 0 part
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Created: 12th Nov 2021 at 23:16
Last updated: 12th Nov 2021 at 23:16
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Version 1 (earliest) Created 12th Nov 2021 at 23:16 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.
Programme: NIBSys
Public web page: http://projects.nib.si/rnainval/
Start date: 1st Nov 2014
End date: 31st Oct 2017
Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_ns-dsRNA_trans, _S_02_metagenome_resp
Assays: _A_01-DNAisol, _A_01_RNA-Seq_dsEGFP-NGS, _A_02-DNASeq, _A_02_CLC-RNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _I_03_Omics-files, _S_01_ns-dsRNA_trans-files, _S_02_metagenome_resp-files
Short Name: 02_metagenome_resp Title: CPB gut microbiome response to dsRNA feeding Description: Response of CPB gut microbiome to dsRNA feeding on the level of microbe abundance Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_03_Omics
Assays: _A_01-DNAisol, _A_02-DNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _S_02_metagenome_resp-files
Short Name: 06_extr_bact-assembly Assay Class: DRY Assay Type: assembly Title: De novo genome assembly of bacteria Description: De novo genome assembly of bacteria from rcf-extracted shotgun metagenomics reads pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
