None
Published Workflows | puva | W2 - Bacterial re-sequencing | Paired-end

Galaxy Workflow ' W2 - Bacterial re-sequencing | Paired-end'

Annotation: Bacterial genome assembly by resequencing using paired-end reads

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: Map with BWA-MEM
Use one from the history
Output dataset 'output' from step 3
Paired-end
Output dataset 'output' from step 1
Output dataset 'output' from step 2
Commonly Used
True
Step 5: SAM-to-BAM
History
Output dataset 'output' from step 4
Output dataset 'output' from step 3
Step 6: BAM to consensus
History
Output dataset 'output1' from step 5
Output dataset 'output' from step 3
False
Step 7: FASTQ to FASTA
Output dataset 'out_fq' from step 6
Step 8: Extract contigs
Output dataset 'output_file' from step 7
300
Step 9: Check bacterial draft
Output dataset 'output_file' from step 7
Output dataset 'output' from step 3
Step 10: Check bacterial contigs
Output dataset 'output' from step 8
Step 11: FASTA Width
Output dataset 'output' from step 8
0
Step 12: SSPACE
Output dataset 'output' from step 11
Output dataset 'output' from step 1
Output dataset 'output' from step 2
FR
False
8
0
select at runtime
0.9
5
0.7
30
200
Step 13: Mugsy
Output dataset 'output' from step 3
Output dataset 'finalscaffolds' from step 12
Step 14: FASTA Width
Output dataset 'finalscaffolds' from step 12
0
Step 15: Check bacterial contigs
Output dataset 'finalscaffolds' from step 12
Step 16: Prokka
Output dataset 'finalscaffolds' from step 12
PROKKA
1
3
No
False
200
Bacteria
11
False
select at runtime
False
False
1e-06
False
False
False
Step 17: MAF to FASTA
Output dataset 'maffile' from step 13
Multiple Blocks
None (value not yet validated)
include blocks with missing species
Step 18: FASTA Width
Output dataset 'out_file1' from step 17
0