Galaxy | Published Workflow | GBS722 VACV-WR 125k - sample denovo with BWASW to ref in hist / UAB

Published Workflows | curtish | GBS722 VACV-WR 125k - sample denovo with BWASW to ref in hist

Annotation: Velvet denovo assembly, with BWA_SW mapping to in-history reference

Step	Annotation
Step 1: Input dataset input select at runtime	FASTA reference genome
Step 2: Input dataset input select at runtime	FASTQsanger FWD
Step 3: Input dataset input select at runtime	FASTQsanger REV
Step 4: velveth Hash Length Not available. Use strand specific transcriptome sequencing False Input Files Input Files 1 file format fastq read type shortPaired reads Dataset Output dataset 'output' from step 2 Input Files 2 file format fastq read type shortPaired2 reads Dataset Output dataset 'output' from step 3
Step 5: velvetg Velvet Dataset Output dataset 'out_file1' from step 4 Generate a AMOS.afg file No Generate a UnusedReads fasta file No Generate velvet LastGraph file No Tracking of short read positions in assembly False Coverage cutoff None Expected Coverage of Unique Regions None Set minimum contig length Yes minimum contig length 200 Using Paired Reads Yes Insert Length in Paired-End Read dataset (ignored when -1) 250 Velvet Advanced Options Use Defaults
Step 6: Unknown Tool with id 'bwasw_demo'
Step 7: SAM-to-BAM Choose the source for the reference genome Use a genome from the history SAM file to convert Output dataset 'output' from step 6 Using reference file Output dataset 'output' from step 1
Step 8: Flagstat BAM File to report statistics of Output dataset 'output1' from step 7