Metavisitor: Workflow for Use Case 2-1

Annotation: DOI: 10.1371/journal.pone.0168397
StepAnnotation
Step 1: Input dataset collection
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Retrieve FASTA from NCBI
NC_001834.1
Nucleotide
False
Step 4: Clip adapter
Output dataset 'output' from step 1
18
50
Fasta format
accept
Use a built-in adapter (select from the list below)
Illumina TruSeq TGGAATTCTCGGGTGCCAAG
Step 5: NCBI BLAST+ makeblastdb
nucleotide
Output dataset 'outfilename' from step 3
DCV NC_001834.1
False
True
select at runtime
Do not assign a Taxonomy ID to the sequences
Step 6: Concatenate datacollection
Output dataset 'output' from step 4
Step 7: fasta - tabular
fasta to tabular
Output dataset 'out_file1' from step 6
Step 8: fasta - tabular
tabular to weighted fasta
Output dataset 'output' from step 7
Step 9: sR_bowtie
Output dataset 'output' from step 8
Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)
2
Use one from the history
select at runtime
tabular
unaligned
Step 10: sR_bowtie
Output dataset 'unaligned' from step 9
Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)
2
Use one from the history
select at runtime
tabular
unaligned
Step 11: sR_bowtie
Output dataset 'unaligned' from step 10
Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)
2
Use one from the history
select at runtime
tabular
unaligned
Step 12: Unknown Tool with id 'toolshed.pasteur.fr/repos/khillion/msp_oases/oasesoptimiserv/0.2.08'
Step 13: NCBI BLAST+ blastx
Output dataset 'transcripts' from step 12
BLAST database from your history
Empty.
Output dataset 'output' from step 2
Empty.
1. Standard
blastx - Traditional BLASTX to compare translated nucleotide query to protein database
0.001
Tabular (select which columns)
qseqid = Query Seq-id (ID of your sequence) sseqid = Subject Seq-id (ID of the database hit) pident = Percentage of identical matches length = Alignment length mismatch = Number of mismatches gapopen = Number of gap openings qstart = Start of alignment in query qend = End of alignment in query sstart = Start of alignment in subject (database hit) send = End of alignment in subject (database hit) evalue = Expectation value (E-value) bitscore = Bit score
slen = Subject sequence length
Nothing selected.
Nothing selected.
Nothing selected.
Hide Advanced Options
Step 14: Parse blast output and compile hits
Output dataset 'transcripts' from step 12
Output dataset 'output1' from step 13
5
extensive
No
Step 15: Pick Fasta sequences
Drosophila_C_virus
Output dataset 'fastaOutput' from step 14
Step 16: Pick Fasta sequences
Cricket_paralysis_virus
Output dataset 'fastaOutput' from step 14
Step 17: Concatenate datasets
Output dataset 'output' from step 15
Datasets
Dataset 1
Output dataset 'output' from step 16
Step 18: cap3
Output dataset 'out_file1' from step 17
40
90
Step 19: NCBI BLAST+ blastx
Output dataset 'contigsandsinglets' from step 18
BLAST database from your history
Empty.
Output dataset 'outfile' from step 5
Empty.
1. Standard
blastx - Traditional BLASTX to compare translated nucleotide query to protein database
0.001
Tabular (select which columns)
qseqid = Query Seq-id (ID of your sequence) sseqid = Subject Seq-id (ID of the database hit) pident = Percentage of identical matches length = Alignment length mismatch = Number of mismatches gapopen = Number of gap openings qstart = Start of alignment in query qend = End of alignment in query sstart = Start of alignment in subject (database hit) send = End of alignment in subject (database hit) evalue = Expectation value (E-value) bitscore = Bit score
slen = Subject sequence length
Nothing selected.
Nothing selected.
Nothing selected.
Hide Advanced Options
Step 20: blast_to_scaffold
Output dataset 'contigsandsinglets' from step 18
Output dataset 'outfilename' from step 3
Output dataset 'output1' from step 19