COVID-19: read pre-processing


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: 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 4: Faster Download and Extract Reads in FASTQ
List of SRA accession, one per line
Output dataset 'output' from step 2
Advanced Options:
Not available.
--split-3: write properly paired biological reads into different files and single reads in another file
True
Step 5: fastp
Paired Collection
Output dataset 'list_paired' from step 3
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
Use default job resource parameters
Step 6: NanoPlot
batch
fastq
Output dataset 'output_collection' from step 4
Options for filtering or transforming input prior to plotting:
Not available.
Not available.
False
Not available.
True
False
False
Not available.
Nothing selected.
False
Options for customizing the plots created:
Nothing selected.
png
Nothing selected.
False
False
Use default job resource parameters
Step 7: FastQC
Output dataset 'output_collection' from step 4
select at runtime
select at runtime
select at runtime
False
Not available.
7
Step 8: Map with minimap2
Use a built-in genome index
hg38
Indexing options:
False
Not available.
Not available.
Not available.
Single
Output dataset 'output_collection' from step 4
Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode.
Set advanced mapping options:
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
False
Not available.
Not available.
Set advanced alignment options:
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
Nothing selected.
Set advanced output options:
BAM
False
False
Not available.
Nothing selected.
False
False
Use default job resource parameters
Step 9: MultiQC
Results
Results 1
fastp
Output dataset 'report_json' from step 5
Empty.
Empty.
False
Step 10: Map with BWA-MEM
Use a built-in genome index
hg38
Paired Collection
Output dataset 'output_paired_coll' from step 5
Empty.
Do not set
1.Simple Illumina mode
Use default job resource parameters
Step 11: MultiQC
Results
Results 1
FastQC
FastQC outputs
FastQC output 1
Raw data
Output dataset 'text_file' from step 7
Empty.
Empty.
False
Step 12: Filter SAM or BAM, output SAM or BAM
Output dataset 'alignment_output' from step 8
Include header
Not available.
yes
The read is unmapped
Nothing selected.
Empty.
Empty.
select at runtime
False
Empty.
BAM (-b)
Step 13: Filter SAM or BAM, output SAM or BAM
Output dataset 'bam_output' from step 10
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 14: MergeSamFiles
Output dataset 'output1' from step 12
False
False
Comments
Lenient
Step 15: MergeSamFiles
Output dataset 'output1' from step 13
False
False
Comments
Lenient
Step 16: Samtools fastx
Output dataset 'outFile' from step 14
FASTQ
Not available.
False
False
unspecific
False
Empty.
no
Nothing selected.
Nothing selected.
Nothing selected.
No
Step 17: Samtools fastx
Output dataset 'outFile' from step 15
FASTQ
Not available.
False
False
READ1 READ2
False
Empty.
no
Nothing selected.
Nothing selected.
Nothing selected.
No