2: Plant virus confirmation
Version 1

Workflow Type: Galaxy
Work-in-progress

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

Inputs

ID Name Description Type
Data_R1.fastq Data_R1.fastq n/a
  • File
Data_R2.fastq Data_R2.fastq n/a
  • File

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
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
reference_fasta reference_fasta n/a
  • File
Read_mapping_alignement Read_mapping_alignement n/a
  • File
mapped_read mapped_read n/a
  • File
Paired-end forward Paired-end forward n/a
  • File
Paired-end reverse Paired-end reverse n/a
  • File
Contigs Contigs n/a
  • File
Log file Log file n/a
  • File
blastn result blastn result n/a
  • File

Version History

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

Added/updated 1 files


Open master 64469c6
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Views: 1524   Downloads: 63

Created: 4th Feb 2021 at 09:10

Last updated: 10th Feb 2023 at 10:06

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Total size: 29.5 KB

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