Sequencing: Protocols and Information
Sequencing

Sequencing

Included here are videos of different aspects of the sequencing process.
Protocol TitleDescription/Goal
Consed & Finishing #1
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What programs we use for phage genome sequencing and finishing, what they do, and where to get them.
Consed & Finishing #7
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How to determine a new phage's cluster: export sequence data from consed, BLAST, then use phagesdb.org to find similar phages.
Consed & Finishing #3
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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 #6
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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 #2
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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 #5
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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 #4
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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.
Assembling Phage Genomes with Newbler
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How to use 454's program Newbler (aka GS De Novo Assembler) to assemble phage genomes that have been sequenced by 454, Ion Torrent, or Illumina technologies. Newbler is installed on the 2013 SEA-PHAGES virtual machine.
Selecting a Subset of Reads From an SFF or FASTQ File
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This video tutorial demonstrates how to take a subset of sequencing reads from an .sff file (454 or Ion Torrent output) or a .fastq file (Illumina output). This can be useful when assembling phage genomes, since NextGen sequencing technologies often return too many reads to get a good assembly for a single phage genome.
Adding .sff or .fastq Reads to an Existing consed Project
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This video tutorial demonstrates how to add reads from an .sff or .fastq file to an existing consed assembly project. This can be useful if only a subset of the reads were used in the initial assembly.