VelvetK

VelvetK optimizes the selection of k-mer size for de novo genome assembly with Velvet using estimated genome size and provided sequence read files.

Key Features:

• K-mer size estimation: Estimates an optimal k-mer size for use with the Velvet assembler based on input data.
• Genome size input options: Accepts an estimated genome size as a numeric value (e.g., 3.5M) or as a FASTA file representing a closely related genome.
• Read file integration: Incorporates all provided sequence read files into the k-mer estimation process.

Scientific Applications:

• De novo genome assembly: Guides k-mer selection to support Velvet-based de novo assembly workflows.
• Assembly parameter optimization: Helps optimize a primary assembly parameter (k-mer) to improve assembly outcomes.
• Comparative-genome-informed estimation: Enables k-mer estimation using a closely related genome FASTA to inform parameter choice.

Methodology:

Computes an optimal k-mer size for Velvet from the estimated genome size (numeric or FASTA of a related genome) together with all provided sequence read files.