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LIsts numberd:
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Day 1: Beginnings and Mapping
Day 2: Calling Genome Variants
- Mapped read data evaluation (SAMtools)
- Installing and compiling tools on Unix
- Integrated pipeline for microbial genome re-sequencing analysis (breseq)
- Calling variants in multiploid genomes and mixed populations (FreeBayes)
- some things to watch out for.
- Comparing variants across samples (VCFtools)
Day 3: RNA-seq
Day 4: Assembly
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Day 4: Assembly
• 90 min de novo assembly: E. coli bacteria –velvet --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)