2: Plant virus confirmation
Version 1

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Run on usegalaxy.eu

Workflow Type: Galaxy

Stable

Mapping against all plant virus then make contig out of the mapped reads then blast them.

SEEK ID: https://workflowhub.eu/workflows/102?version=1

Inputs

ID	Name	Description	Type
batchmode	batchmode	runtime parameter for tool FASTA Merge Files and Filter Unique Sequences	n/a
Data_R1.fastq	Data_R1.fastq	n/a	n/a
Data_R2.fastq	Data_R2.fastq	n/a	n/a
fastq_input	fastq_input	runtime parameter for tool Map with minimap2	n/a
fastq_input	fastq_input	runtime parameter for tool Map with minimap2	n/a
reference_source	reference_source	runtime parameter for tool Map with minimap2	n/a
excludebed	excludebed	runtime parameter for tool BAM filter	n/a
includebed	includebed	runtime parameter for tool BAM filter	n/a
infile	infile	runtime parameter for tool BAM filter	n/a
input	input	runtime parameter for tool Samtools stats	n/a
inputFile	inputFile	runtime parameter for tool SamToFastq	n/a
library	library	runtime parameter for tool Shovill	n/a
library	library	runtime parameter for tool Shovill	n/a
output	output	runtime parameter for tool NCBI BLAST+ blastn	n/a
output	output	runtime parameter for tool NCBI BLAST+ blastn	n/a
output	output	runtime parameter for tool NCBI BLAST+ blastn	n/a
query	query	runtime parameter for tool NCBI BLAST+ blastn	n/a

Steps

ID	Name	Description
0	Merge fasta together	Merge several fasta in a multi-fasta file to be use as reference for mapping. WARNING: If two fasta with the same header are provided only one will be kept toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
1	Data_R1.fastq
2	Data_R2.fastq
3	Map with minimap2	Map the input reads against the chosen reference fasta file. Multiple mapping The correct placement of a read may be ambiguous, e.g. due to repeats. In this case, there may be multiple read alignments for the same read. One of these alignments is considered primary. All the other alignments have the secondary alignment flag set in the SAM records that represent them. All the SAM records have the same QNAME and the same values for 0x40 and 0x80 flags. Typically the alignment designated primary is the best alignment, but the decision may be arbitrary. toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2
4	BAM filter	Keep only mapped read to perform faster assembly later. toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9
5	Samtools stats	Obtain stats on the bam file toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
6	SamToFastq	Extract read from bam as fastq sequence. Remove secondary alignement reads (that are mapped several time) toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2
7	Fast assembly (shovill => megahit)	Make contig out of candidate read. toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0
8	BLASTn	Blast contig against precise database to find closest reference toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0

Outputs

ID	Name	Description	Type
output	output	n/a	fasta
alignment_output	alignment_output	n/a	bam
outfile	outfile	n/a	bam
output	output	n/a	tabular
fq_single	fq_single	n/a	fastqsanger
interleaved_fastq	interleaved_fastq	n/a	fastqsanger
fq1	fq1	n/a	fastqsanger
fq2	fq2	n/a	fastqsanger
fq_u	fq_u	n/a	fastqsanger
shovill_std_log	shovill_std_log	n/a	txt
contigs	contigs	n/a	fasta
contigs_graph	contigs_graph	n/a	txt
output1	output1	n/a	tabular

Creators and Submitter

Creators

Not specified

Submitter

johan Rollin

License

Apache Software License 2.0

Activity

Views: 240 Downloads: 22

Created: 4th Feb 2021 at 09:10

Last used: 18th Sep 2021 at 15:12

Version History

Version 1 Created 4th Feb 2021 at 09:10 by johan Rollin

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2: Plant virus confirmation Version 1