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Day 4: Assembly
• 90 min de novo assembly: E. coli bacteria --velvet (Aaron), mira (refguided Aaron), Allpaths(-LG) (Scott – optional..), mention: abyss, SOAPdenovo
• 30 min Finding and annotating genes – maker, glimmer; web tools: JCVI, NCBI, psi-blast & CDD; pfam/rfam (Scott & Jeff)
• 45 min Evaluating & visualizing assemblies – Comparing: treat assembler output as a reference genome and proceed with prior tools – challenges: contigs, errors; Visualizing: mauve, circos (may need install help) (Scott); cgview (Jeff).
• 30 Genome databases: Introduction to GMOD and/or SequenceServer (can we standup web servers on the class computers?) (Scott)
Notes from 5/17/12:
Conventions decided on - expands for hints, formats for command prompt/code
Aaron to write .sge maker script
All qsub's will run "./commands"
All examples have to have a "commands" file.