| Protocol Title | Last Modified | Description |
| Consed & Finishing #1 View Video |
Nov 14, 2011 | What programs we use for phage genome sequencing and finishing, what they do, and where to get them. |
| Consed & Finishing #2 View Video |
Nov 14, 2011 | How to use the basic UNIX commands pwd, ls, and cd to navigate through your files from a command-line prompt. Consed will be run from the command line, so knowing these is a prerequisite. |
| Consed & Finishing #3 View Video |
Nov 14, 2011 | A look at the standard directory structure for consed projects, and how to run consed for a particular project from the command line. |
| Consed & Finishing #4 View Video |
Nov 14, 2011 | The basics of consed. What to look for in the Main Window, the Assembly View, and the Aligned Reads window. How to open a Sanger chromatogram trace file. |
| Consed & Finishing #5 View Video |
Nov 14, 2011 | Opening a Newbler-assembled project in consed, looking at 454 data in Assembly and Aligned Reads views, and making sure you can see 454 "traces." |
| Consed & Finishing #6 View Video |
Nov 14, 2011 | The first things to do when you get a new assembly project back: checking the number of contigs and coverage and finding weak areas. |
| Consed & Finishing #7 View Video |
Nov 14, 2011 | How to determine a new phage's cluster: export sequence data from consed, BLAST, then use phagesdb.org to find similar phages. |