Assembly using Tophat2 and annotation Version 1
Visit source
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Open
Stable
Alignment, assembly and annotation of generated transcripts from RNASEQ reads.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| List of Illumina accessions | List of Illumina accessions | n/a |
|
| Reference annotation | Reference annotation | n/a |
|
| Reference genome. | Reference genome. | n/a |
|
| SARS-CoV-2 proteins | SARS-CoV-2 proteins | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | UniProt | toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.1.0 |
| 5 | Illumina data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4 |
| 6 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 7 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 8 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
| 9 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 10 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
| 11 | Filter SAM or BAM, output SAM or BAM | toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1 |
| 12 | Illumina filtered reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
| 13 | TopHat | toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1 |
| 14 | Cufflinks | toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2 |
| 15 | Cuffmerge | toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1 |
| 16 | Cuffquant | toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.1 |
| 17 | Cuffdiff | toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5 |
| 18 | gffread | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2 |
| 19 | TransDecoder | toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1 |
| 20 | Antismash | toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1 |
| 21 | Glimmer ICM builder | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2 |
| 22 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 23 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
| 24 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
| 25 | jackhmmer | toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0 |
| 26 | Glimmer3 | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2 |
| 27 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
| _anonymous_output_10 | _anonymous_output_10 | n/a |
|
| _anonymous_output_11 | _anonymous_output_11 | n/a |
|
| _anonymous_output_12 | _anonymous_output_12 | n/a |
|
| _anonymous_output_13 | _anonymous_output_13 | n/a |
|
| _anonymous_output_14 | _anonymous_output_14 | n/a |
|
| _anonymous_output_15 | _anonymous_output_15 | n/a |
|
| fastq | fastq | n/a |
|
| fast | fast | n/a |
|
| _anonymous_output_16 | _anonymous_output_16 | n/a |
|
| _anonymous_output_17 | _anonymous_output_17 | n/a |
|
| _anonymous_output_18 | _anonymous_output_18 | n/a |
|
| _anonymous_output_19 | _anonymous_output_19 | n/a |
|
| _anonymous_output_20 | _anonymous_output_20 | n/a |
|
| _anonymous_output_21 | _anonymous_output_21 | n/a |
|
| _anonymous_output_22 | _anonymous_output_22 | n/a |
|
| _anonymous_output_23 | _anonymous_output_23 | n/a |
|
| _anonymous_output_24 | _anonymous_output_24 | n/a |
|
| _anonymous_output_25 | _anonymous_output_25 | n/a |
|
| _anonymous_output_26 | _anonymous_output_26 | n/a |
|
| _anonymous_output_27 | _anonymous_output_27 | n/a |
|
| _anonymous_output_28 | _anonymous_output_28 | n/a |
|
| _anonymous_output_29 | _anonymous_output_29 | n/a |
|
| _anonymous_output_30 | _anonymous_output_30 | n/a |
|
| _anonymous_output_31 | _anonymous_output_31 | n/a |
|
| _anonymous_output_32 | _anonymous_output_32 | n/a |
|
| _anonymous_output_33 | _anonymous_output_33 | n/a |
|
| _anonymous_output_34 | _anonymous_output_34 | n/a |
|
| _anonymous_output_35 | _anonymous_output_35 | n/a |
|
| _anonymous_output_36 | _anonymous_output_36 | n/a |
|
| _anonymous_output_37 | _anonymous_output_37 | n/a |
|
| _anonymous_output_38 | _anonymous_output_38 | n/a |
|
| fasta | fasta | n/a |
|
| _anonymous_output_39 | _anonymous_output_39 | n/a |
|
| _anonymous_output_40 | _anonymous_output_40 | n/a |
|
| _anonymous_output_41 | _anonymous_output_41 | n/a |
|
| _anonymous_output_42 | _anonymous_output_42 | n/a |
|
| _anonymous_output_43 | _anonymous_output_43 | n/a |
|
| _anonymous_output_44 | _anonymous_output_44 | n/a |
|
| _anonymous_output_45 | _anonymous_output_45 | n/a |
|
| _anonymous_output_46 | _anonymous_output_46 | n/a |
|
| _anonymous_output_47 | _anonymous_output_47 | n/a |
|
| _anonymous_output_48 | _anonymous_output_48 | n/a |
|
| _anonymous_output_49 | _anonymous_output_49 | n/a |
|
| _anonymous_output_50 | _anonymous_output_50 | n/a |
|
| _anonymous_output_51 | _anonymous_output_51 | n/a |
|
| _anonymous_output_52 | _anonymous_output_52 | n/a |
|
| _anonymous_output_53 | _anonymous_output_53 | n/a |
|
| _anonymous_output_54 | _anonymous_output_54 | n/a |
|
| _anonymous_output_55 | _anonymous_output_55 | n/a |
|
| _anonymous_output_56 | _anonymous_output_56 | n/a |
|
| _anonymous_output_57 | _anonymous_output_57 | n/a |
|
| _anonymous_output_58 | _anonymous_output_58 | n/a |
|
Version History
Version 1 (earliest) Created 18th Jun 2020 at 00:17 by Ambarish Kumar
Added/updated 2 files
Open
master7e5d993
Creators and Submitter
Tools
License
Activity
Views: 5089 Downloads: 862 Runs: 4
Created: 18th Jun 2020 at 00:17
Last updated: 1st Jul 2020 at 09:55
AttributionsNone
Related items
Advanced Spaces list for this Workflow with search and filtering
The goal of COVID-19-Biohackathon 2020 (COVID-19-BH20) is to develop and gather computational tools that can be useful for studying the biology of the virus and the disease.
The COVID-19 Programme in Workflow Hub aims to gather workflows for the analysis of COVID-19 molecular biology data and their metadata. In this programme, all workflows and their metadata will be curated and made interoperable, reusable and reproducible. All workflows and their metadata will be easily accessible to everyone ...
Teams: Connor Lab, GalaxyProject SARS-CoV-2, InSaFLU, nf-core viralrecon, CWL workflow SARS-CoV-2, V-Pipe, Test team
Web page: https://github.com/virtual-biohackathons/covid-19-bh20
Advanced Teams list for this Workflow with search and filtering
Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org
Space: COVID-19 Biohackathon
Public web page: https://github.com/galaxyproject/SARS-CoV-2
