Metavisitor: Workflow for Use Case 1-3

Created: 2016-05-13 08:11:43 Last updated: 2017-04-17 15:44:12

Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence data
Readthedoc
Mississippi Galaxy server

Not currently available.

Inputs (2)

Name	Description
Input Dataset Collection
viral nucleotide BLAST database (NCBI 19-10-2015)

Steps (16)

Name	Tool	Description
Input dataset collection	None
Input dataset	None
NCBI BLAST+ blastn	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08
Parse blast output and compile hits	toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3
cap3	toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0
NCBI BLAST+ blastn	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08
blast_to_scaffold	toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0
Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0
Retrieve FASTA from NCBI	toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.4
Clip adapter	toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6
NCBI BLAST+ makeblastdb	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08
Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2
Normalize By Median	toolshed.g2.bx.psu.edu/repos/iuc/khmer_normalize_by_median/khmer_normalize_by_median/2.0.0
Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2
sRbowtie	toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1
Oases_optimiser	toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.2.1

Outputs (29)