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

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Views: 47 Downloads: 1
Created: 4th Feb 2021 at 09:10
Last used: 7th Mar 2021 at 03:15

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