Note:

This page has been discontinued. Please see this page instead.

Mapping

• Mapping with bowtie2
• Calculate Coverage from BAM file
• Separating mapped and unmapped reads from libraries
• From exonerate to igv: A story about GFF

PacBio SMRT data

• Using PBJelly to gap-close scaffolds
• Using short reads to correct long reads with ECtools
• Using short reads to correct long reads with LSC
• Using short reads to correct long reads with PacBioToCA
• correct uncorrected ECtools reads with LSC

Misc. programs

• Tobias UCE tutorial
• Using SpeciesGeoCoder
• Creating bacterial phylogenetic trees with PhyloPhlAn

Best practices

• Check your downloads with md5sum
• Starting a new bioinformatics project
• Downloading and storing data on Albiorix
• Submitting data to SRA

Transcriptome Quality-Evaluation

• A simple Transrate tutorial