StringTie assembly and annotation
Version 1

Workflow Type: Galaxy
Stable

Alignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.

Inputs

ID Name Description Type
List of Illumina accessions List of Illumina accessions n/a
  • File
Reference genome Reference genome n/a
  • File
Reference genome annotation Reference genome annotation n/a
  • File
SARS-CoV-2 proteins SARS-CoV-2 proteins n/a
  • File

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 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
fasta fasta n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
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_anonymous_output_6 _anonymous_output_6 n/a
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_anonymous_output_7 _anonymous_output_7 n/a
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_anonymous_output_8 _anonymous_output_8 n/a
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_anonymous_output_9 _anonymous_output_9 n/a
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_anonymous_output_10 _anonymous_output_10 n/a
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_anonymous_output_11 _anonymous_output_11 n/a
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_anonymous_output_12 _anonymous_output_12 n/a
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_anonymous_output_13 _anonymous_output_13 n/a
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_anonymous_output_14 _anonymous_output_14 n/a
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_anonymous_output_15 _anonymous_output_15 n/a
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_anonymous_output_16 _anonymous_output_16 n/a
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_anonymous_output_17 _anonymous_output_17 n/a
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_anonymous_output_18 _anonymous_output_18 n/a
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_anonymous_output_19 _anonymous_output_19 n/a
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_anonymous_output_20 _anonymous_output_20 n/a
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_anonymous_output_21 _anonymous_output_21 n/a
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_anonymous_output_22 _anonymous_output_22 n/a
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_anonymous_output_23 _anonymous_output_23 n/a
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_anonymous_output_24 _anonymous_output_24 n/a
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_anonymous_output_25 _anonymous_output_25 n/a
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_anonymous_output_26 _anonymous_output_26 n/a
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_anonymous_output_27 _anonymous_output_27 n/a
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_anonymous_output_28 _anonymous_output_28 n/a
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_anonymous_output_29 _anonymous_output_29 n/a
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_anonymous_output_30 _anonymous_output_30 n/a
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_anonymous_output_31 _anonymous_output_31 n/a
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_anonymous_output_32 _anonymous_output_32 n/a
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_anonymous_output_33 _anonymous_output_33 n/a
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_anonymous_output_34 _anonymous_output_34 n/a
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_anonymous_output_35 _anonymous_output_35 n/a
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_anonymous_output_36 _anonymous_output_36 n/a
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_anonymous_output_37 _anonymous_output_37 n/a
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_anonymous_output_38 _anonymous_output_38 n/a
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_anonymous_output_39 _anonymous_output_39 n/a
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_anonymous_output_40 _anonymous_output_40 n/a
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_anonymous_output_41 _anonymous_output_41 n/a
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_anonymous_output_42 _anonymous_output_42 n/a
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_anonymous_output_43 _anonymous_output_43 n/a
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Version History

Version 1 (earliest) Created 18th Jun 2020 at 00:13 by Ambarish Kumar

Added/updated 2 files


Open master b358d9f
help Creators and Submitter
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Views: 2293   Downloads: 83

Created: 18th Jun 2020 at 00:13

Last updated: 1st Jul 2020 at 09:57

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