COVID-19: Unicycler assembly and annotation


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: UniProt
A Common Organism
9606
Nothing selected.
fasta
Step 4: Faster Download and Extract Reads in FASTQ
List of SRA accession, one per line
Output dataset 'output' from step 1
Advanced Options:
Not available.
--split-3: write properly paired biological reads into different files and single reads in another file
True
Step 5: NCBI BLAST+ makeblastdb
protein
Output dataset 'output' from step 2
Empty.
False
True
select at runtime
Do not assign a Taxonomy ID to the sequences
Step 6: NCBI BLAST+ makeblastdb
protein
Output dataset 'proteome' from step 3
Empty.
False
True
select at runtime
Do not assign a Taxonomy ID to the sequences
Step 7: fastp
Paired Collection
Output dataset 'list_paired' from step 4
Adapter Trimming Options:
False
Empty.
Empty.
Global trimming options:
Not available.
Not available.
Not available.
Not available.
Overrepresented Sequence Analysis:
False
Not available.
Filter Options:
Quality filtering options:
False
20
20
Not available.
Length filtering options:
False
50
Low complexity filtering options:
False
Not available.
Read Modification Options:
Automatic trimming for Illumina NextSeq/NovaSeq data
Not available.
Disable polyX trimming
UMI processing:
False
Empty.
Not available.
Empty.
Per read cutting by quality options:
False
False
Not available.
Not available.
Base correction by overlap analysis options:
False
Output Options:
True
True
Step 8: Map with BWA-MEM
Use a built-in genome index
hg38
Paired Collection
Output dataset 'output_paired_coll' from step 7
Empty.
Do not set
1.Simple Illumina mode
Step 9: MultiQC
Results
Results 1
fastp
Output dataset 'report_json' from step 7
Empty.
Empty.
False
Step 10: Filter SAM or BAM, output SAM or BAM
Output dataset 'bam_output' from step 8
Include header
Not available.
yes
The read is unmapped The mate is unmapped
Nothing selected.
Empty.
Empty.
select at runtime
False
Empty.
BAM (-b)
Step 11: Samtools fastx
Output dataset 'output1' from step 10
FASTQ
Not available.
False
False
READ1 READ2
False
Empty.
no
Nothing selected.
Nothing selected.
Nothing selected.
No
Step 12: MergeSamFiles
Output dataset 'output1' from step 10
False
False
Comments
Lenient
Step 13: Samtools fastx
Output dataset 'outFile' from step 12
FASTQ
Not available.
False
False
READ1 READ2
False
Empty.
no
Nothing selected.
Nothing selected.
Nothing selected.
No
Step 14: Create assemblies with Unicycler
Paired
Output dataset 'forward' from step 13
Output dataset 'reverse' from step 13
select at runtime
Normal (moderate contig size and misassembly rate)
10000
1
Not available.
SPAdes options:
False
0.2
0.95
Empty.
10
0.25
False
Rotation options:
False
select at runtime
90.0
95.0
Pilon options:
False
1000
Graph cleaning options:
1000
1000
Long read alignment parameters:
select at runtime
3,-6,-5,-2
Not available.
Step 15: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2'
Step 16: Antismash
Output dataset 'assembly' from step 14
Bacteria
Nucleotide
True
True
True
True
True
True
True
False
True
HTML file All results EMBL files GenBank files Gene clusters
Step 17: TransDecoder
Output dataset 'assembly' from step 14
50
Advanced Options:
False
universal
Not available.
900
False
Training Options:
Train with the top longest ORFs
500
Step 18: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2'
Step 19: jackhmmer
Output dataset 'transdecoder_pep' from step 17
5
Output dataset 'proteome' from step 3
Table of per-sequence hits (--tblout) Table of per-domain hits (--domtblout)
False
False
False
Disable
10.0
10.0
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
False
0.02
0.001
1e-05
False
Assign columns with >= symfrac residues as consensus (--fast)
0.5
0.5
Henikoff position-based weights (--wpb)
Disabled
Unspecified
200
200
200
200
100
200
0.04
False
Not available.
Not available.
42
Step 20: NCBI BLAST+ makeblastdb
protein
Output dataset 'transdecoder_pep' from step 17
Empty.
False
True
select at runtime
Do not assign a Taxonomy ID to the sequences
Step 21: NCBI BLAST+ blastp
Output dataset 'transdecoder_pep' from step 17
BLAST database from your history
Empty.
Output dataset 'outfile' from step 6
Empty.
blastp - Traditional BLASTP to compare a protein query to a protein database
0.001
Tabular (extended 25 columns)
Hide Advanced Options
Step 22: NCBI BLAST+ blastp
Output dataset 'transdecoder_pep' from step 17
BLAST database from your history
Empty.
Output dataset 'outfile' from step 5
Empty.
blastp - Traditional BLASTP to compare a protein query to a protein database
0.001
Tabular (extended 25 columns)
Hide Advanced Options
Step 23: NCBI BLAST+ blastp
Output dataset 'proteome' from step 3
BLAST database from your history
Empty.
Output dataset 'outfile' from step 20
Empty.
blastp - Traditional BLASTP to compare a protein query to a protein database
0.001
Tabular (extended 25 columns)
Hide Advanced Options