2: Plant virus confirmation
Version 1

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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Created: 4th Feb 2021 at 09:10

Last used: 7th Mar 2021 at 03:15

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

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