[PDF] fastp: an ultra-fast all-in-one FASTQ preprocessor | Semantic Scholar (2024)

Atria matches the adapters in paired reads and finds possible overlapped regions with a super-fast and carefully designed byte-based matching algorithm (O(n) time with O(1) space) that can be used in a broad range of short-sequence matching applications.

Ktrim was ∼2-18 times faster than current tools and also showed high accuracy when applied on the testing datasets and could serve as a valuable and efficient tool for short-read NGS data preprocessing.

RabbitFX is a fast, efficient, and easy-to-use framework for processing biological sequencing data on modern multi-core platforms that can efficiently read FASTA and FASTQ files by combining a lightweight parsing method by means of an optimized formatting implementation.

FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes and is an all-in-one software that is convenient for bulk data analysis.

RabbitQCPlus is an ultra-efficient quality control tool for modern multi-core systems that uses vectorization, memory copy reduction, parallel (de)compression, and optimized data structures to achieve substantial performance gains.

A suite of tools, called SeqFu (Sequence Fastx utilities), that provides a broad range of commands to perform both common and specialist operations with ease and is designed to be easily implemented in high-performance analytical pipelines.

This work proposes the first FPGA-based framework dubbed FAST to accelerate the stages that deal with sequence trimming, in particular adapter and primer removal, which supports a comprehensive set of functionalities and is convenient to use by operating on standard genomics data formats.

A set of fast and accurate adapter detection and trimming algorithms that entail no a priori adapter sequences are introduced that are particularly useful in meta-analyses of a large batch of datasets and can be incorporated in any sequence analysis pipelines in all scales.

Falco is presented, an emulation of the popular FastQC tool that runs on average three times faster while generating equivalent results and requires less memory to run and provides more flexible visualization of HTML reports.

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SOAPnuke is demonstrated as a tool with abundant functions for a “QC-Preprocess-QC” workflow and MapReduce acceleration framework that enables large scalability to distribute all the processing works to an entire compute cluster.

Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.

Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations.

The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.

Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

The SpeedSeq platform accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement.

It is shown that errors in the UMI sequence are common and network-based methods to account for these errors when identifying PCR duplicates are introduced, demonstrating the value of properly accounting for errors in UMIs.

A detailed protocol for efficient DS adapter synthesis, library preparation and target enrichment, as well as an overview of the data analysis workflow are provided.

The authors' tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome, and a software package GenomeHalving is created based on this new algorithm, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.

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