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Published Workflows | puva | W5 - Metagenomics

Galaxy Workflow ' W5 - Metagenomics'

Annotation: Metagenomics analysis

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Rename sequences
Output dataset 'output' from step 1
Numeric Counter
Rename sequences in order to remove 'strange' characters from read name (i.e. ':')
Step 3: FASTQ to FASTA
Output dataset 'output' from step 2
Step 4: MetaPhlAn
Output dataset 'output_file' from step 3
profiling a metagenomes in terms of relative abundances
all taxonomic levels
Very Sensitive Local
Step 5: NCBI BLAST+ blastn
Output dataset 'output_file' from step 3
Locally installed BLAST database
megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences
1e-05
Tabular (extended 25 columns)
Show Advanced Options
True
Both
0
0.0
64
True
False
Step 6: Krona pie chart
Output dataset 'output' from step 4
Step 7: Filter
Output dataset 'output1' from step 5
(c4/c23)>0.5
0
Filter suboptimal sequence alignments using the expression (sequence_alignment_length/sequence_read_length > 0.5 ); sequences that do not meet this criterion are filtered out
Step 8: Cut
c1,c2
Tab
Output dataset 'out_file1' from step 7
Step 9: Convert
Pipes
Output dataset 'out_file1' from step 8
True

No value found for 'Strip leading and trailing whitespaces', used default

True

No value found for 'Condense consecutive delimiters in one TAB', used default

Step 10: Cut
c1,c3
Tab
Output dataset 'out_file1' from step 9
Step 11: Fetch taxonomic representation
Output dataset 'out_file1' from step 10
2 (value not yet validated)
1 (value not yet validated)
Step 12: Find lowest diagnostic rank
Output dataset 'out_file1' from step 11
No restriction
Step 13: Filter taxonomy
Output dataset 'out_file1' from step 12
0.5
Step 14: Krona pie chart
Output dataset 'out_file1' from step 12
Step 15: Summarize taxonomy
Output dataset 'output' from step 13
Step 16: Draw phylogeny
Output dataset 'output' from step 13
Show entire tree
Normal
0