BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data

Abstract

Bioinformatic analysis—such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, file format conversion, and processing and analysis—is integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses, but unified toolkits that conduct all these analyses are lacking. To address this gap, we introduce BioKIT, a versatile command line toolkit that has, upon publication, 42 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we conducted a comprehensive examination of relative synonymous codon usage across 171 fungal genomes that use alternative genetic codes, showed that the novel metric of gene-wise relative synonymous codon usage can accurately estimate gene-wise codon optimization, evaluated the quality and characteristics of 901 eukaryotic genome assemblies, and calculated alignment summary statistics for 10 phylogenomic data matrices. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/jlsteenwyk-biokit/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT).

COVID-19-Associated Pulmonary Aspergillosis Isolates Are Genomically Diverse but Similar to Each Other in Their Responses to Infection-Relevant Stresses

“…To obtain high-quality and adapter-free reads, raw reads were trimmed with Trimmomatic version 0.39 ( 39 ) using the parameters “2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.” On average, 36 million read pairs passed trimming. Trimmed reads were then assembled with SPAdes version 3.15.2 ( 40 ) using the parameters “–isolate” and “–cov-cutoff auto.” Genome statistics were calculated with BioKIT version 0.0.4 ( 41 ).…”

“…To align the 4,515 single-copy orthologs, MAFFT version 7.402 ( 46 , 47 ) was used along with the parameters “-bl 62 -op 1.0 -maxiterate 1000 -retree 1 -genafpair” ( 41 ). The 4,515 alignments were trimmed with version 1.2.0 of ClipKIT ( 22 ) and then combined into a supermatrix with PhyKIT version 1.5.0 ( 51 ).…”

OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

“…Archival instabilities among software threatens the reproducibility of bioinformatics research [ 60 ]. To ensure long-term stability of OrthoSNAP, we implemented previously established rigorous development practices and design principles [ 44 , 52 , 61 , 62 ]. For example, OrthoSNAP features a refactored codebase, which facilitates debugging, testing, and future development.…”

Phylogenomics reveals extensive misidentification of fungal strains from the genusAspergillus

“…The resulting supermatrix had 6,378,237 sites (2,846,432 parsimony informative sites). Alignment length and number of parsimony informative sites were calculated using BioKIT, v0.1.2 (Steenwyk et al, 2022). IQ-TREE 2 was used for tree inference (Minh et al, 2020, 2).…”