BioKIT

BioKIT provides 40 sequence-analysis functions that process genome assemblies, multiple sequence alignments, coding sequences, and sequencing data for bioinformatics analyses.

Key Features:

• Function set: Forty diverse functions for routine and novel processing tasks across genome assemblies, multiple sequence alignments, coding sequences, and sequencing data.
• Genome assembly quality assessment: Computes assembly quality and characteristic metrics for genome assemblies.
• Alignment summary statistics: Calculates summary statistics for multiple sequence alignments and phylogenomic data matrices.
• Relative synonymous codon usage (RSCU): Calculates RSCU across coding sequences, including a gene-wise relative synonymous codon usage metric.
• Gene-wise RSCU metric: Implements a novel gene-wise relative synonymous codon usage metric to estimate gene-wise codon optimization.
• Paired-end aware quality trimming: Performs paired-end aware quality trimming of sequencing reads.
• Sequencing read filtering: Filters sequencing reads according to specified criteria.
• File format conversion: Converts between common bioinformatics file formats.
• Community-sourced functions: Incorporates community-sourced functions to extend analytical capabilities.
• Other bioinformatics tasks: Provides additional essential sequence analysis tasks for routine workflows.

Scientific Applications:

• Eukaryotic genome assessment: Used to assess the quality and characteristics of 901 eukaryotic genome assemblies.
• Phylogenomic alignment statistics: Used to calculate alignment summary statistics for 10 phylogenomic data matrices.
• Codon usage analysis: Used to determine relative synonymous codon usage across 171 fungal genomes.
• Codon optimization metric: Introduced a gene-wise RSCU metric to estimate gene-wise codon optimization.

Methodology:

Performs genome assembly quality assessment, computes alignment summary statistics, calculates relative synonymous codon usage including gene-wise RSCU, executes paired-end aware quality trimming and sequencing read filtering, and performs file format conversion.