Below is a compilation of resources that I often refer to for various purposes – from data visualization to sequence format conversion. With any luck, they’ll be as helpful to you as they have been to me!
Data visualization in R
General sequence data manipulation
via the command line
sam/bam manipulation: Dave Tang’s excellent repo of samtools commands
biom manipulation: format conversion; metadata supplementation
via the web
multiple sequence alignment (MSA) conversion: ALTER – a convenient web interface for MSA format conversion (especially good with phylip)
MSA and unaligned format conversion: Los Alamos National Lab’s sequence format converter (good for aligned or unaligned)
16S/18S sequence annotation
default dada2-formatted reference databases
Statistics
an excellent resource for diving into statistical learning, from the masters