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Published Workflows | yinan | viramp_workflow_pe

Galaxy Workflow ' viramp_workflow_pe'

Annotation: A demo to connect individual tools provided in the viramp platform into a complete viramp working pipeline
StepAnnotation
Step 1: Input dataset
select at runtime
Read-1 in paired end datasets
Step 2: Input dataset
select at runtime
Read-2 in paired-end dataset
Step 3: Input dataset
select at runtime
Reference genome
Step 4: Trim Sequence by Quality
Output dataset 'output' from step 1
30
Step 5: Trim Sequence by Quality
Output dataset 'output' from step 2
30
Step 6: Merge Pair
Output dataset 'output' from step 4
Output dataset 'output' from step 5
Step 7: Reduce the coverage
Output dataset 'output' from step 6
paired end
10
4
1e8
Step 8: Velvet
Interleaved paired-end reads AND Single-end reads
Output dataset 'peoutput' from step 7
Output dataset 'seoutput' from step 7
35,45,55,65
Step 9: Reference-guided Scaffolding
Output dataset 'output' from step 8
Output dataset 'output' from step 3
Step 10: Scaffolding pre-assembled contigs using paired-read data
Output dataset 'output' from step 9
Output dataset 'output' from step 4
Output dataset 'output' from step 5
350
FASTA
Default Settings
Step 11: Quality Assessment For Genome Assembling
Output dataset 'output' from step 3
Output dataset 'sspace_res' from step 10
500
Step 12: SNV detection
Output dataset 'output' from step 3
Output dataset 'sspace_res' from step 10
Step 13: Create Circos Graph for Draft Genome Assemblies visualization
Output dataset 'output' from step 3
Output dataset 'sspace_res' from step 10
Step 14: Draft vs. Reference genome comparison
Output dataset 'output' from step 3
Output dataset 'sspace_res' from step 10
Reference Coordinates