StringTie assembly and annotation Version 1
Visit source
Download RO Crate
Run on usegalaxy.euAlignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| mask_data_file | mask_data_file | runtime parameter for tool NCBI BLAST+ makeblastdb | n/a |
| mask_data_file | mask_data_file | runtime parameter for tool NCBI BLAST+ makeblastdb | n/a |
| bed_file | bed_file | runtime parameter for tool Filter SAM or BAM, output SAM or BAM | n/a |
| chr_replace | chr_replace | runtime parameter for tool gffread | n/a |
| mask_data_file | mask_data_file | runtime parameter for tool NCBI BLAST+ makeblastdb | n/a |
Steps
| ID | Name | Description |
|---|---|---|
| 0 | List of Illumina accessions | |
| 1 | Reference genome | |
| 2 | Reference genome annotation | |
| 3 | UniProt | toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.1.0 |
| 4 | SARS-CoV-2 proteins | |
| 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 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
| 10 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 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 | HISAT2 | toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5 |
| 14 | StringTie | toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1 |
| 15 | StringTie merge | toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1 |
| 16 | gffread | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2 |
| 17 | Glimmer ICM builder | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2 |
| 18 | Antismash | toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1 |
| 19 | TransDecoder | toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1 |
| 20 | Glimmer3 | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2 |
| 21 | jackhmmer | toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0 |
| 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 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| proteome | proteome | n/a | uniprotxml |
| list_paired | list_paired | n/a | input |
| output_collection | output_collection | n/a | input |
| output_collection_other | output_collection_other | n/a | input |
| log | log | n/a | txt |
| outfile | outfile | n/a | data |
| outfile | outfile | n/a | data |
| output_paired_coll | output_paired_coll | n/a | input |
| report_html | report_html | n/a | html |
| report_json | report_json | n/a | json |
| stats | stats | n/a | input |
| html_report | html_report | n/a | html |
| bam_output | bam_output | n/a | bam |
| output1 | output1 | n/a | sam |
| forward | forward | n/a | fasta |
| reverse | reverse | n/a | fasta |
| output_alignments | output_alignments | n/a | bam |
| output_gtf | output_gtf | n/a | gtf |
| coverage | coverage | n/a | gtf |
| gene_counts | gene_counts | n/a | tabular |
| transcript_counts | transcript_counts | n/a | tabular |
| out_gtf | out_gtf | n/a | gtf |
| output_exons | output_exons | n/a | fasta |
| outfile | outfile | n/a | data |
| genecluster_tabular | genecluster_tabular | n/a | input |
| genbank | genbank | n/a | input |
| embl | embl | n/a | input |
| archive | archive | n/a | input |
| html | html | n/a | html |
| transdecoder_pep | transdecoder_pep | n/a | fasta |
| transdecoder_cds | transdecoder_cds | n/a | fasta |
| transdecoder_bed | transdecoder_bed | n/a | bed |
| transdecoder_gff3 | transdecoder_gff3 | n/a | gff3 |
| genes_output | genes_output | n/a | fasta |
| report_output | report_output | n/a | txt |
| detailed_output | detailed_output | n/a | txt |
| output | output | n/a | txt |
| tblout | tblout | n/a | txt |
| domtblout | domtblout | n/a | txt |
| outfile | outfile | n/a | data |
| output1 | output1 | n/a | tabular |
| output1 | output1 | n/a | tabular |
| output1 | output1 | n/a | tabular |
Creators and Submitter
Views: 514 Downloads: 43
Created: 18th Jun 2020 at 00:13
Last updated: 1st Jul 2020 at 09:57
Last used: 16th Apr 2021 at 16:08
AttributionsNone
Version History
Version 1 Created 18th Jun 2020 at 00:13 by Ambarish Kumar
No revision comments
Related items
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
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
