Introduction

Large-scale biological data analysis often involves many domain-specific tools chained together in order to obtain meaningful results. The handling of workflows is a well-known problem in computer science, and many software have been specifically developed. For instance, Galaxy [1], Taverna [2], GeneProf [3] and Sequanix [4] are user-friendly GUI-based interfaces aimed at creating custom pipelines for non-programmer users. At the same time, other solutions have been developed for more advanced users to provide more control over operations using existing general-purpose programming languages or domain-specific languages (DSL). Ruffus [5] pipelines are created using the Python language, Pwrake [6] and GXP Make [7] are based on the existing DSL Rake and Make. BigDataScript [8], Bpipe [9] and SnakeMake [10] are examples of languages specifically designed for the development of bioinformatics pipelines, aiming at the maximum flexibility and powerfulness without the steeper learning curve of a general-purpose programming language. It is worth noting that Sequanix is a GUI to SnakeMake, demonstrating that it is possible to obtain high accessibility without sacrificing flexibility and powerfulness. There are other systems that can be used to create reliable workflows, but they have slightly different aims or they are difficult to extend with new tools [11].

Nevertheless, all these approaches suffer some limitations. First, samples from different sources have to be analysed with similar approaches but with specific implementations. This problem could be solved by performing small sample-specific modifications to the pipeline to obtain the desired results. This approach is highly error-prone, as every change made to the pipeline might introduce new errors producing inconsistent results. Moreover, the possibility to multiplex many NGS experiments in a single sequencing run introduces the need to perform different analyses with different parameters on distinct files.

To tackle these issues, we here introduce HaTSPiL, a python-based pipeline for high-throughput sequencing data analyses designed with the idea of being modular, flexible and expandable. HaTSPiL automatises all steps of an NGS analysis through the use of a barcoding system encoding all the required information, thus minimising user’s intervention. HaTSPiL is based on two layers: a core layer responsible for the execution of all the parts of the workflow and an external layer that defines each step of the pipeline. To show the functionality of HaTSPiL, we set it up to perform mutation analysis on DNA sequencing data (i.e. whole exome or targeted gene sequencing). HaTSPiL can be easily modified by users to customise solutions and extend the capabilities of the software.

Materials and methods

Results

HaTSPiL was developed to solve practical problems related to NGS data analysis, being its usability and reliability the highest priority of the project. The tool comes with a bundled workflow for mutation analysis of DNA-sequencing experiments (both whole exome or whole genome sequencing) and it has been successfully run on different types of tumours, xenografts, blood derived samples and cell organoids. The software automatically matches the tumour samples with the relative control samples to improve the detection of somatic mutations. The workflow relies on the utilisation of widely used software in order to take advantage of the state-of-the-art solutions available to date. On the other hand, specific cases required the development of custom analysis scripts (Fig 1).

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Fig 1. A schematic representation of the workflow of HaTSPiL.

The topmost left part shows the starting point of the whole analysis, a set of barcoded FastQ files. The software supports the most common operations to handle the data, performing different steps of filtering and alignment. It is shown that the various steps can change depending on the barcoding of the sample, and that the workflow is highly customisable. At date, HaTSPiL supports a mutation analysis pipeline, and this feature will be improved and extended. Additional analysis pipeline can be added easily as well, and a final step of report generation is included, in order to provide an immediate and user-friendly output.

https://doi.org/10.1371/journal.pone.0222512.g001

HaTSPiL can also automatically generate reports, thus providing a user-friendly interface to check results. For every set of input files, interactive plots are created to show the quality and the coverage of the samples (Fig 2A). Graphical comparisons between samples and relative controls are shown when available (Fig 2B). An interactive table with the damaging mutations found by the variant calling process is also shown, highlighting the genes that are known to be druggable (Fig 2C). HaTSPiL is also capable of reading all the data stored during previous analyses and to generate a summary for every sequencing, layering the information by sample, biopsy, patient and project. This simple representation provides the user with an overview of the experiments across a large timescale, facilitating the detection of problems and biases for specific sequencing experiments.

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Fig 2. Representation of the output in a report automatically generated by HaTSPiL.

(A) Two of the plots showing the quality of a single sequencing. The values are obtained using Picard software (https://broadinstitute.github.io/picard/). (B) Two comparisons between samples and relative control. This representation is used with a scalable amount of samples, from a single sample to all the samples available for a whole project. A control sample is always added, if available, in order to provide a minimal comparison against another sequencing. (C) A portion of the table containing the mutations found highly damaging by the variant calling. The mutated genes that are known to be a target of a drug are highlighted.

https://doi.org/10.1371/journal.pone.0222512.g002

Discussion

The high customisability and modularity of HaTSPiL allows the implementation of many steps that can be useful for the user, even if the aim is different from mutation analysis. Adapter trimming is performed through Cutadapt [13], which can be run for both single- and paired-end sequencing and which uses the parameters specified in the config.ini file. The FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) is run to produce a glimpse of the overall sequencing quality, then a quality trimming is performed through SeqKit [14] to avoid common quality loss at the start and the end of the reads. HaTPSiL then performs a sequence alignment using one of the supported software: NovoAlign (http://www.novocraft.com/products/novoalign/) or BWA [15] for DNA-based sequencing, or STAR [16] for RNA-seq analyses. It is also possible to handle xenograft samples, which require a step aimed at splitting the reads belonging to the tumour from those belonging to the avatar animal, using either Xenome [17] or Disambiguate [18]. The data obtained from the alignment step is then refined using GATK [19] and Picard (https://broadinstitute.github.io/picard/) in order to perform indel realignment, base recalibration, removal of duplicates and collection of statistics. All the described steps are common to many different NGS analysis pipelines, therefore HaTSPiL can be extremely useful in a large number of situations, even without any need for user customisation. Moreover, a mutation analysis procedure is automatically run using Mutect [20], VarScan [21] and Strelka [22], by automatically changing the behaviour of the workflow and the used parameters depending on the presence of control samples. The mutations found by these software are further evaluated and filtered using a previously published method, which allows the integration of clinical information from curated databases as Cosmic [23], dbSNP [24] and ClinVar [25].

Conclusion

HaTSPiL is a powerful workflow engine for next-generation sequencing data analysis, aiming at higher reliability, modularity and reproducibility. The approach is orthogonal to other existing systems for the automation of chained bioinformatics operations, and the software is designed to be used in different fields, from pure research to health-related projects. The software is designed to be easily employed by both non-experienced (as a ready-to-use pipeline) and experienced users (due to its great customisability and extendibility). It is worth noting that the large API and the database interoperability allow for the creation of third-party software that can take advantage of the reliability of the engine. HaTSPiL will continuously improve, through the integration of many different NGS data analysis tools and workflows. In future releases we will expand HaTSPil through the integration of new features and better support for auxiliary software.

Supporting information