ArticleGenetics2022
BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data.
Article in Genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Thiamine cross-feeding drives microbial coexistence in the leaf microbiome.Nature microbiology · 2026Article
- Horizontal transfer of accessory chromosomes in fungi - a regulated process for exchange of genetic material?Heredity · 2026Review
- Chloroplast and Mitochondrial Genomes of the Lichen-Symbiotic Green Alga Trebouxia Illuminate Evolutionary Relationships and Climate Associations and Yield New Phylogenetic Markers.Genome biology and evolution · 2026Article
- Regions of low gene expression promote maintenance and adaptation of horizontally acquired genes in yeasts.Communications biology · 2026Article
- Article
- Transposable elements hitchhike on Starships across fungal genomes.Nature communications · 2026Article
- Genomic and physiological signatures of adaptation in pathogenic fungi.Nature communications · 2026Article
- Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Temperature variability and other climatic attributes linked to genomic features in the lichen-forming fungal genus Umbilicaria.BMC biology · 2025Article
- ClipKIT in the browser: fast online trimming of multiple sequence alignments for phylogenetics.Nucleic acids research · 2025Article
- Three reference genomes for freshwater diatom ecology and evolution.Journal of phycology · 2025Article
- Evolutionary origin and population diversity of a cryptic hybrid pathogen.Nature communications · 2024Article
- Diverse signatures of convergent evolution in cactus-associated yeasts.PLoS biology · 2024Article
- Article
- The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi.G3 (Bethesda, Md.) · 2024Article
- Phylogenomics reveals extensive misidentification of fungal strains from the genusMicrobiology spectrum · 2024Article
- Diverse signatures of convergent evolution in cacti-associated yeasts.bioRxiv : the preprint server for biology · 2023Article
- Isolation, characterization, and evaluation of putative new bacteriophages for controlling bacterial spot on tomato in Brazil.Archives of virology · 2023Article
- Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen.bioRxiv : the preprint server for biology · 2023Article
- Identification of the Neoaspergillic Acid Biosynthesis Gene Cluster by Establishing anACS omega · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
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).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.