Unicycler assembly and annotation
Version 1

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 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
bam_output bam_output n/a bam
stats stats n/a input
html_report html_report n/a html
output1 output1 n/a sam
forward forward n/a fasta
reverse reverse n/a fasta
outFile outFile n/a bam
forward forward n/a fasta
reverse reverse n/a fasta
assembly_graph assembly_graph n/a tabular
assembly assembly 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
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
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Views: 296   Downloads: 19

Created: 18th Jun 2020 at 00:07

Last updated: 1st Jul 2020 at 10:00

Last used: 21st Oct 2020 at 11:12

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