The FAIRDOMHub

25 items tagged with 'bash'.

Gudrun Gygli

Well rounded biologist/biotechnologist/biochemist/enzymologist/bioinformatician/computational biologist.

Alex Bossers

Projects: Not specified

Institutions: Not specified

https://orcid.org/0000-0002-6586-717X

Expertise: Bioinformatics, Molecular Biology, Next Generation Sequencing, metagenomics, Proteomics, Programming

Tools: bash, Perl, R, Genomics, Proteomics, Biochemistry and protein analysis

Research scientist in multi-Omics, molecular (cell)biology and bioinformatics.

Thomas Hentrich

Projects: ICYSB 2015 - International Practical Course in Systems Biology

Institutions: University of Tübingen

Expertise: Bioinformatics, Software Engineering, Epigenomics, Biomolecular Computing, NGS analysis

Tools: Java, Matlab, bash, linux

Trained as a Computer Scientist at the University of Jena, Germany, my interests drifted more and more towards "computing life" during my PhD at Simon Fraser University and the University of British Columbia, Canada. On one hand, that term captures that I got fascinated by the idea to understand life as a form of computation and to describe, reprogram, and reassemble parts of cells as described in many brilliant experiments from a spectrum of disciplines ranging from DNA computing to Synthetic

...

Antoine Buetti-Dinh

Projects: SysMetEx, Kinetics on the move - Workshop 2016

Institutions: Università della Svizzera Italiana

Expertise: ODE modelling of biological interaction network, Bioinformatics

Tools: Python, c++, Java, bash, standard bioinformatic tools

http://tinyurl.com/jgget87

_A_05_BUSCO

_p_stRT

Assay: A05_BUSCO

Short Name: 05_BUSCO

Assay Class: DRY

Assay Type: BUSCO

Title: BUSCO post filtering and reassignment

Description: BUSCO post filtering and reassignment

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1173.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar, /transfer/transfer.zip

Created: 7th Nov 2019 at 18:11, Last updated: 16th Nov 2019 at 12:08

_A_04_TransRate

_p_stRT

Assay: A04_TransRate

Short Name: 04_TransRate

Assay Class: DRY

Assay Type: TransRate

Title: TransRate post filtering and reassignment

Description: TransRate post filtering and reassignment

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1172.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output.tar, /scripts/run_TransRate_commands.sh

Created: 7th Nov 2019 at 18:09, Last updated: 16th Nov 2019 at 12:22

_A_03.2_components

_p_stRT

Assay: A03.2_components

Short Name: 03.2_components

Assay Class: DRY

Assay Type: components

Title: Components: tr2aacds headers, cdhit-2d

Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters

pISA Assay creation date: 2019-10-22

pISA Assay creator: Ziva Ramsak

Phenodata: None

Featuredata:

Data:

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1171.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_4_cdhit-2d.tar.gz, /output/output.tar, /scripts/scripts.tar

Created: 7th Nov 2019 at 18:06, Last updated: 15th Nov 2019 at 21:07

_A_03.1_filtering

_p_stRT

Assay: A03.1_filtering

Short Name: 03.1_filtering

Assay Class: DRY

Assay Type: filtering

Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs

Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1170.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate/intermediate.tar, /output/Desiree_tr.cds.tsv.gz, /output/PW363_tr.cds.tsv.gz, /output/Rywal_tr.cds.tsv.gz, /output/other/output_full.tar.gz, /output/other/output_summary.tar.gz, /reports/03.1_Rywal_combo_withFiltering.html, /reports/03.2_PW363_combo_withFiltering.html, /reports/03.3_Desiree_combo_withFiltering.html, /reports/SupplementaryTableS3, /reports/SupplementaryTableS4, /reports/SupplementaryTableS5, /scripts/scripts.tar

Created: 7th Nov 2019 at 18:04, Last updated: 18th Mar 2020 at 19:37

_A_02.8_DIAMOND

_p_stRT

Assay: A02.8_DIAMOND

Short Name: 02.8_DIAMOND

Assay Class: DRY

Assay Type: DIAMOND

Title: DIAMOND on raw tr2aacds output

Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1169.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Created: 7th Nov 2019 at 18:02, Last updated: 16th Nov 2019 at 12:28

_A_02.7_VecScreen

_p_stRT

Assay: A02.7_VecScreen

Short Name: 02.7_VecScreen

Assay Class: DRY

Assay Type: VecScreen

Title: VecScreen on raw tr2aacds output

Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1168.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl

Created: 7th Nov 2019 at 17:58, Last updated: 16th Nov 2019 at 12:37

_A_02.6_TransRate

_p_stRT

Assay: A02.6_TransRate

Short Name: 02.6_TransRate

Assay Class: DRY

Assay Type: TransRate

Title: TransRate stat on raw tr2aacds transcriptomes

Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: Nonde

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1167.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Created: 7th Nov 2019 at 17:54, Last updated: 16th Nov 2019 at 12:45

_A_02.4_STAR

_p_stRT

Assay: A02.4_STAR

Short Name: 02.4_STAR

Assay Class: DRY

Assay Type: STAR

Title: mapping reads back to evigene .tr output

Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map

pISA Assay creation date: 2019-10-22

pISA Assay creator: Marko Petek

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt

Created: 7th Nov 2019 at 17:48, Last updated: 2nd Jun 2020 at 15:42

_A_02.5_STARlong_matchAnnot

_p_stRT

Assay: A02.5STARlongmatchAnnot

Short Name: 02.5STARlongmatchAnnot

Assay Class: DRY

Assay Type: matchAnnot

Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations

Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations

pISA Assay creation date: 2019-10-22

pISA Assay creator: Marko Petek

Phenodata: None

Featuredata: None

...

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den...

Created: 7th Nov 2019 at 17:50, Last updated: 16th Nov 2019 at 12:55

_A_02.3_InterProScan

_p_stRT

Assay: A02.3_InterProScan

Short Name: 02.3_InterProScan

Assay Class: DRY

Assay Type: InterProScan

Title: InterProScan on tr2aacds output

Description: InterProScan on tr2aacds output

pISA Assay creation date: 2019-10-22

pISA Assay creator: Marko Petek

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd

Created: 7th Nov 2019 at 17:46, Last updated: 16th Nov 2019 at 13:35

_A_02.2_assembly-contribution-count

_p_stRT

Assay: A02.2_assembly-contribution-count

Short Name: 02.2_assembly-contribution-count

Assay Class: DRY

Assay Type: count

Title: assembly contribution count

Description: assembly contribution count, input/output tr2aacds

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1163.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /output/output.tar, /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryTableS6, /scripts/scripts.tar

Created: 7th Nov 2019 at 17:04, Last updated: 26th Feb 2020 at 14:00

_A_02.1_BUSCO

_p_stRT

Assay: A02.1_BUSCO

Short Name: 02.1_BUSCO

Assay Class: DRY

Assay Type: BUSCO

Title: BUSCO on assemblies and tr2aacds output

Description: BUSCO on assemblies and tr2aacds output

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1162.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Created: 7th Nov 2019 at 16:57, Last updated: 16th Nov 2019 at 13:40

_A_01_evigene

_p_stRT

Assay: A01_evigene

Short Name: 01_evigene

Assay Class: DRY

Assay Type: evigene

Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11

Description: See http://eugenes.org/EvidentialGene/about/EvidentialGenetrassemblypipe.html

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Integration

Snapshots: Snapshot 1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_Rywal.tar.gz, /output/output.tar, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Created: 7th Nov 2019 at 16:54, Last updated: 16th Nov 2019 at 14:21

Analysis Version 1.5

Simulation Foundries

This is the analysis part of the Simulation Foundry, Version 1.5.

Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name.

Launch the bash script, following the instructions in the manual.

Make sure you followed the instructions in "Preparation" before running this.

Submitter: Gudrun Gygli

Biological problem addressed: various analyses of molecular dynamics simulations

Snapshots: No snapshots

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Organisms: No organisms

Models: No Models

SOPs: ANALYSIS_1.5

Data files: No Data files

Created: 24th Oct 2019 at 11:31, Last updated: 7th Nov 2019 at 13:28

Simulation Version 1.5

Simulation Foundries

This is the simulation part of the Simulation Foundry, Version 1.5.

Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name.

Launch the bash script, following the instructions in the manual.

Make sure you followed the instructions in "Preparation" before running this.

Submitter: Gudrun Gygli

Assay type: Molecular Dynamics

Technology type: All-Atom

Snapshots: No snapshots

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Organisms: No organisms

SOPs: SIMULATIONS_V1.5

Data files: No Data files

Created: 24th Oct 2019 at 11:17, Last updated: 7th Nov 2019 at 13:28

Preparation

Simulation Foundries

Preparation needed to use Simulation Foundry, Version 1.5.

Please read the manual before working with this Simulation Foundry.

Pay careful attention to the installation instructions.

Note the known issues.

Submitter: Gudrun Gygli

Assay type: Instructions

Technology type: Technical Computer Installation

Snapshots: No snapshots

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Organisms: No organisms

SOPs: No SOPs

Data files: Installation Instructions

Created: 24th Oct 2019 at 09:57, Last updated: 7th Nov 2019 at 13:28

ANALYSIS_1.5

Simulation Foundries

Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry.

Make sure you followed "Preparations" instructions!

Read the Manual!

Creator: Gudrun Gygli

Submitter: Gudrun Gygli

Investigations: 1 hidden item

Studies: Simulation Foundry for Methanol-Water Mixtures

Assays: Analysis Version 1.5

Download

Created: 24th Oct 2019 at 11:33, Last updated: 7th Nov 2019 at 13:28

SIMULATIONS_V1.5

Simulation Foundries

Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry.

Make sure you followed "Preparations" instructions!

Read the Manual!

Creator: Gudrun Gygli

Submitter: Gudrun Gygli

Investigations: 1 hidden item

Studies: Simulation Foundry for Methanol-Water Mixtures

Assays: Simulation Version 1.5

Download

Created: 24th Oct 2019 at 11:21, Last updated: 7th Nov 2019 at 13:28

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

_p_stRT

(Show All)

Abstract (Expand)

Background: Although the reference genome of Solanum tuberosum group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid group … Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research and its subsequent applications in breeding. Results: For the DM genome assembly, two only partially-overlapping gene models exist differing in a unique set of genes and intron/exon structure predictions. First step was to merge and manually curate the merged gene model, creating a union of genes in Phureja scaffold. We next compiled available RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using CLC, Trinity, Velvet, and rnaSPAdes de novo assemblers using different settings to test for optimal outcome. In addition, for cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. Revised EvidentialGene redundancy-reducing pipeline was employed to produce accurate and complete cultivar-specific transcriptomes from assemblers output, as well as to attain the pan-transcriptome. Due to being the most diverse dataset in terms of tissues (stem, seedlings and roots) and experimental conditions, cv. Désirée was the most complete transcriptome (95.8% BUSCO completeness). For cv. Rywal and breeding clone PW363 data were available for leaf samples only and the resulting transcriptomes were less complete than cv. Désirée (89.8% and 89.3% BUSCO completeness, respectively). Cross comparison of these cultivar-specific transcriptomes and merged DM gene model suggests that the core potato transcriptome is comprised of 16,339 genes. The pan-transcriptome contains a total of 95,779 transcripts, of which 54,614 transcripts are not present in the Phureja genome. These represent the variants of the novel genes found in the potato pan-genome. Conclusions: Our analysis shows that the available gene model of double-monoploid potato from group Phureja is, to some degree, not complete. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput -omics analyses, and future breeding programmes.

Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden

Date Published: No date defined

Publication Type: Not specified

DOI: 10.1101/845818

Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Created: 19th Nov 2019 at 12:48, Last updated: 19th Nov 2019 at 12:57