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SeqKit2: A Swiss army knife for sequence and alignment processing
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DOI：10.1002/imt2.191.png)
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Abstract
En 中文
In the era of ubiquitous high-throughput sequencing studies, there is a growing need for analysis tools that are not just performant but also comprehensive and user-friendly enough to cater to both novice and advanced users. This article introduces SeqKit2, the next iteration of the widely used sequence analysis tool SeqKit, featuring expanded functionality, performance optimizations, and support for additional compression methods. Retaining a pragmatic subcommand architecture, SeqKit2 represents substantial enhancement through the inclusion of 19 additional subcommands, expanding its overall repertoire to a total of 38 in eight categories. The new subcommands add functionality such as amplicon processing and robust, error-tolerant parsing of sequence records. In addition, three subcommands designed for real-time analysis are added for periodic monitoring of properties of FASTQ and Binary Alignment/Map alignment records and real-time streaming from multiple sequence files. The performance of SeqKit2 is benchmarked against the old version of SeqKit, Bioawk, Seqtk, and SeqFu tools. SeqKit2 consistently outperforms its predecessor, albeit with marginally higher memory usage, while maintaining competitive runtimes against other tools. With its broad functionality, proven usability, and ongoing development driven by user feedback, we hope that bioinformaticians will find SeqKit2 useful as a Swiss army knife of sequence and alignment processing-equally adept at facilitating ad hoc analyses and seamlessly integrating into larger pipelines. SeqKit2 has significantly expanded its capabilities, doubling the number of subcommands from 19 to 38, and adding support for three more compression file formats. This enhances its versatility and efficiency in sequence and alignment processing. Benchmarking results demonstrate that SeqKit2 consistently outperforms its predecessor and remains competitive with other similar tools. In addition, SeqKit2 has notably improved user-friendliness with the introduction of new features, such as autocompletion for subcommands and command-line flags and enhanced error-handling mechanisms. image SeqKit2 expands its capabilities, doubling the number of subcommands from 19 to 38, and adding support for three more compression file formats. SeqKit2 outperforms its predecessor and maintains competitive with other tools. SeqKit2 improves user-friendliness with new features, like, autocompletion, progress bars, and enhanced error handling.
Keywords:
performance optimization
real-time analysis
sequence processing
usability
user-friendly
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