This codebook.txt file was generated on  20190325 by Chris Shaffer


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GENERAL INFORMATION
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1. Title of Dataset

Genome Assembly of phage JustBecause

2. Author Information


 Principal Investigator 
Christopher Shaffer
Box 1137; Dept of Biology
Washington University in St. Louis
St. Louis MO 63130

shaffer@wustl.edu

3. Date of data collection (single date, range, approximate date)
Fall 2017


4. Geographic location of data collection (where was data collected?): 

Phage isolated 38.645708 N, 90.311579 W

5. Information about funding sources that supported the collection of the data:

Supported in part by the Biology Dept Washgington University and by Howard Hughes Medical Institute, Chevy Chase MD

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SHARING/ACCESS INFORMATION
-------------------------- 


1. Licenses/restrictions placed on the data: 
No restrictions on use


2. Links to publications that cite or use the data:
<TBD - citation to paper>

3. Links to other publicly accessible locations of the data:
NA


4. Links/relationships to ancillary data sets:
http://phagesdb.org/phages/JustBecause


5. Was data derived from another source?
          NA


6. Recommended citation for the data:
<TBD - citation to paper>

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DATA & FILE OVERVIEW
---------------------

1. File List
   A. Filename:        finishing_notes_on_assembly.txt
      Short description:        Comments and analysis results for genome assembly


        
   B. Filename:        JustBecause_fasta
      Short description:        Final DNA sequence for phage Satis


        
   C. Filename:        justbecuase_100k.fastq
      Short description:        raw read data of genome in fastq format

   D.  Filename: justbecause_coverage.png
       Short description:  visualization

   E. Filename: justbecause_alignment.png
        Short description:  visualization

   C. Filename:        justbecuase_assembly (level 2 sub-folder)
      Short description: Folder with all 
	subfolders and files properly organized for use with Consed:
        	
		454AlignmentInfo.tsv
		454AllContigs.fna
		454AllContigs.qual
		454AssemblyProject.xml
		454ContigGraph.txt
		454LargeContigs.fna
		454LargeContigs.qual
		454NewblerMetrics.txt
		454NewblerProgress.txt
		454PairStatus.txt
		454ReadStatus.txt
		454Scaffolds.fna
		454Scaffolds.qual
		454Scaffolds.txt
		454TrimStatus.txt
		consed (level 3 sub-folder)
			chromat_dir (level 4 sub-folder)
				[empty]
			edit_dir (level 4 subfolder)
				phd.ball
				justbecause_right.fasta
				justbecause_left.fasta
				justbecause_draft.fasta
				contig00001.fasta
				badLibraries.txt
				454Contigs.ace.3.wrk
				454Contigs.ace.3
				454Contigs.ace.2.wrk
				454Contigs.ace.2
				454Contigs.ace.1.wrk
				454Contigs.ace.1
				454Contigs.ace.0
			phd_dir (level 4 subfolder)
	
				[empty]




2. Relationship between files:        
All files pertain to the sequencing and assembly of phage JustBecause.



3. Additional related data collected that was not included in the current data package:

NA


4. Are there multiple versions of the dataset? NO
   

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METHODOLOGICAL INFORMATION
--------------------------


1. Description of methods used for collection/generation of data: 
 Genome assembly of Illumina MiSeq reads using Newbler. Complete consed package created. 


2. Methods for processing the data: 
Assembly by Newbler (commercial software no longer available) 


3. Instrument- or software-specific information needed to interpret the data:
Visualization and assessment of assembly by Consed version 25, see:
Gordon and Green. 2013. Consed: A Graphical Editor for Next-Generation Sequencing. Bioinformatics. Volume 29 Number 22 pp.2936-2937.


4. Standards and calibration information, if appropriate:
NA

5. Environmental/experimental conditions:
NA


6. Describe any quality-assurance procedures performed on the data:
NA



7. People involved with sample collection, processing, analysis and/or submission:
Saransh Gothi 
John H. Alarcon
Kelly Hartigan
Christopher Shaffer