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Published Workflows | puva | W3 - Bacterial de novo assembly | Paired-end

Galaxy Workflow ' W3 - Bacterial de novo assembly | Paired-end'

Annotation: Bacterial genome assembly by de novo approach using paired-end reads

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: FASTQ interlacer
Output dataset 'output' from step 1
Output dataset 'output' from step 2
Step 4: velveth
False
Input Files
Input Files 1
fastq
shortPaired reads
Output dataset 'outfile_pairs' from step 3
Step 5: velveth
False
Input Files
Input Files 1
fastq
shortPaired reads
Output dataset 'outfile_pairs' from step 3
Step 6: velveth
False
Input Files
Input Files 1
fastq
shortPaired reads
Output dataset 'outfile_pairs' from step 3
Step 7: Abyss
Output dataset 'outfile_pairs' from step 3
Step 8: spades
False
False
True
21,33,55
Library
Libraries 1
Paired-end / Single reads
-> <- (fr)
Files
Files 1
Interleaved files
Output dataset 'outfile_pairs' from step 3
Step 9: velvetg
Output dataset 'out_file1' from step 4
No
Yes
No
No
True
Automatically Determined
Automatically Determined
Yes
200
Yes
Use Defaults
Step 10: velvetg
Output dataset 'out_file1' from step 5
No
Yes
No
No
True
Automatically Determined
Automatically Determined
Yes
200
Yes
Use Defaults
Step 11: velvetg
Output dataset 'out_file1' from step 6
No
Yes
No
No
True
Automatically Determined
Automatically Determined
Yes
200
Yes
Use Defaults
Step 12: Concatenate datasets
Output dataset 'contigs' from step 9
Datasets
Dataset 1
Output dataset 'contigs' from step 10
Dataset 2
Output dataset 'contigs' from step 11
Step 13: CD-HIT
Output dataset 'out_file1' from step 12
nucleotides (cd-hit-est)
True
1.0
8
Step 14: CISA Contigs Integrator
Contigs files
Contigs file 1
Output dataset 'fasta_out' from step 13
Contigs file 2
Output dataset 'outfile' from step 7
Contigs file 3
Output dataset 'out_contigs' from step 8
100
11
Step 15: Check bacterial contigs
Output dataset 'outfile' from step 14
Step 16: FASTA Width
Output dataset 'outfile' from step 14
100
Step 17: Prokka
Output dataset 'outfile' from step 14
PROKKA
1
3
No
False
200
Bacteria
11
False
select at runtime
False
False
1e-06
False
False
False