Introduction, no hands on exercises this meeting.
PRINSEQ was used for quality trimming and data analysis (link to standalone version is here).
Alignment programs used are bowtie2 and bwa-mem. Also required are samtools and the R package rbamtools.
Velvet is required for assembly.
RSEM and bowtie2 (see above) are required, in addition to an R script provided on the course site.
SAMtools (see above), bcftools and the R package VariantAnnotation are used. Note that this R package can be quite difficult to install.
No additional programs are required for this exercise.
BLAST2GO was used for GO annotation, along with HMMER2GO. Ontologizer is used for GO term enrichment. Also, a Bash script was provided to automate the GO annotation process.
All exercises are done with the Seaview application.
Wrap up discussion and lecture on phylogenomics, no hands on exercises.