Table 1.

Inputs and parameters that can be specified for each of PlasticDB’s tools

Tool	Input	Parameters
Annotate Gene	A FASTA or FASTQ file containing one sequence in nucleotide or amino acid format. Files can contain assembled or raw reads and be uncompressed or compressed using gzip.	File type, BLAST type, e-value, percent identity and microorganism type.
Annotate Genome	A FASTA or FASTQ file containing multiple sequences in nucleotide or amino acid format. Files can contain assembled or raw reads and be uncompressed or compressed using gzip.	File type, BLAST type, e-value, percent identity and microorganism type.
Annotate Taxa Table	A taxa table file containing at least genus and species names.	Field separator, genus column, species column.
Compare Genomes	Multiple FASTA or FASTQ files containing multiple sequences in nucleotide or amino acid format. Files can contain assembled or raw reads and be uncompressed or compressed using gzip.	File type, BLAST type, e-value and percent identity.
Pathway Analysis	A FASTA or FASTQ file containing multiple sequences in nucleotide or amino acid format. Files can contain assembled or raw reads and be uncompressed or compressed using gzip.	File type, BLAST type, e-value and percent identity.