VSG_Pipeline

Organization Structure

To start:

Current Directory{ Pipeline.py VSGFunctions.py [SequencingFile1].fastq [SequencingFile2].fastq }

When Finished:

Current Directory{ Pipeline.py VSGFunctions.py [SequencingFile1].fastq [SequencingFile2].fastq [Y-M-D-H_M]-[OptionalDescriptiveHeaderNames]{ # "Header" [SequencingFile1]{ [SequencingFile1]_trimmed2.fq } [SequencingFile2]{ [SequencingFile2]_trimmed2.fq }

	[Header]_[SequencingFile1]_contig.fa
	[Header]_[SequencingFile1]_orf_clean.fa
	[Header]_[SequencingFile1]_orf_trans_clean.fa
	[Header]_[SequencingFile1]_orf_trans.fa
	[Header]_[SequencingFile1]_orf_VSGs_scores.txt
	[Header]_[SequencingFile1]_orf_VSGs.fa
	[Header]_[SequencingFile1]_orf.fa
	[Header]_[SequencingFile2]_contig.fa
	[Header]_[SequencingFile2]_orf_clean.fa
	[Header]_[SequencingFile2]_orf_trans_clean.fa
	[Header]_[SequencingFile2]_orf_trans.fa
	[Header]_[SequencingFile2]_orf_VSGs_scores.txt
	[Header]_[SequencingFile2]_orf_VSGs.fa
	[Header]_[SequencingFile2]_orf.fa
	[Header]_orf_VSGs_merged.fa
	[Header]_orf_VSGs.fa 

	[Header]_[SequencingFile1]_orf.xml
	[Header]_[SequencingFile2]_orf.xml

	[SequencingFile1]_MULTo.txt
	[SequencingFile1]_Trinity.Trinity.fasta
	[SequencingFile2]_MULTo.txt
	[SequencingFile2]_Trinity.Trinity.fasta
	[Header]_orf_VSGs_merged.fa.clstr
	
	[SequencingFile1]_align.sam
	[SequencingFile2]_align.sam
}

}