Workflow Type: Galaxy
Open
Stable
Alignment, assembly RNASEQ reads and annotation of generated transcripts.
Inputs
ID | Name | Description | Type |
---|---|---|---|
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 |
lr_align | lr_align | runtime parameter for tool Create assemblies with Unicycler | n/a |
long | long | runtime parameter for tool Create assemblies with Unicycler | n/a |
rotation | rotation | runtime parameter for tool Create assemblies with Unicycler | n/a |
input | input | runtime parameter for tool TransDecoder | 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 | SARS-CoV-2 proteins | |
2 | UniProt | toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.1.0 |
3 | Illumina data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4 |
4 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
5 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
6 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
7 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
8 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
9 | Filter SAM or BAM, output SAM or BAM | toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1 |
10 | Illumina filtered reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
11 | MergeSamFiles | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1 |
12 | Illumina filtered and merged reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
13 | Unicycler assembly | toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 |
14 | Glimmer ICM builder | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2 |
15 | Antismash | toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1 |
16 | TransDecoder | toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1 |
17 | Glimmer3 | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2 |
18 | jackhmmer | toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0 |
19 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
20 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
21 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
22 | 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 | |
list_paired | list_paired | n/a | |
output_collection | output_collection | n/a | |
output_collection_other | output_collection_other | n/a | |
log | log | n/a | |
outfile | outfile | n/a | |
outfile | outfile | n/a | |
output_paired_coll | output_paired_coll | n/a | |
report_html | report_html | n/a | |
report_json | report_json | n/a | |
bam_output | bam_output | n/a | |
stats | stats | n/a | |
html_report | html_report | n/a | |
output1 | output1 | n/a | |
forward | forward | n/a | |
reverse | reverse | n/a | |
outFile | outFile | n/a | |
forward | forward | n/a | |
reverse | reverse | n/a | |
assembly_graph | assembly_graph | n/a | |
assembly | assembly | n/a | |
outfile | outfile | n/a | |
genecluster_tabular | genecluster_tabular | n/a | |
genbank | genbank | n/a | |
embl | embl | n/a | |
archive | archive | n/a | |
html | html | n/a | |
transdecoder_pep | transdecoder_pep | n/a | |
transdecoder_cds | transdecoder_cds | n/a | |
transdecoder_bed | transdecoder_bed | n/a | |
transdecoder_gff3 | transdecoder_gff3 | n/a | |
genes_output | genes_output | n/a | |
output | output | n/a | |
tblout | tblout | n/a | |
domtblout | domtblout | n/a | |
outfile | outfile | n/a | |
output1 | output1 | n/a | |
output1 | output1 | n/a | |
output1 | output1 | n/a |
Version History
Version 1 (earliest) Created 18th Jun 2020 at 00:07 by Ambarish Kumar
Added/updated 2 files
Open
master
27e1a69

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Activity
Views: 2131 Downloads: 74
Created: 18th Jun 2020 at 00:07
Last updated: 1st Jul 2020 at 10:00
Last used: 25th Jun 2022 at 10:21

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