roadmap

IO

sequence formats

• FASTA
• FASTQ
• GenBank
• EMBL

Loads more at http://www.bioperl.org/wiki/HOWTO:SeqIO, but many of these are antiquated formats. I think we should prioritise by popularity. The sooner BioJulia is useful the better for the community.

annotation formats

• GFF & GTF (this is messy in most languages - it would be great if we could cleanly handle all the quirks)
• BED
• VCF

alignment formats

• BLAST (tabular/long form)
• MultiFASTA aligned
• CLUSTAL
• BAM/SAM
• Phylip
• PFAM

tree formats

• Newick (can be ported from Phylogenetics.jl)
• Nexus
• PhyloXML

also database connectors, for e.g. BioSQL

datastructures

We'll want to have representations of:

• DNA, RNA and amino acid sequences
• ranges and features of sequences (where the sequence may or may not be present)
• alignments - pairwise and multiple
• graph-derivative structures like phylogenetic trees, genetic networks and biochemical pathways
• probabilistic models of sequences (e.g. motifs - perhaps this isn't a high priority)

tool wrappers

• BLAST
• Blat
• bowtie/2
• bwa
• HMMER
• Primer3
• Phylogenetic tools (clustal, mafft, PAML, phylip)
• samtools (unless we can do something faster in our own sam/bam implementation)
• signalP/targetP
• assemblers: velvet/oases, trinity, soapdenovo

service APIs

• BioMart
• Ensembl
• EMBL
• NCBI
• SRA

datasets

• genome sequences
• genome annotations
• gene ontologies