MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2024-04-24 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae061

Jose L Figueroa, Andrew Redinbo, Ajay Panyala, Sean Colby, Maren L Friesen, Lisa Tiemann, Richard Allen White

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引用次数: 0

Abstract

Motivation: MerCat2 ("Mer-Catenate2") is a versatile, parallel, scalable and modular property software package for robustly analyzing features in omics data. Using massively parallel sequencing raw reads, assembled contigs, and protein sequences from any platform as input, MerCat2 performs k-mer counting of any length k, resulting in feature abundance counts tables, quality control reports, protein feature metrics, and graphical representation (i.e. principal component analysis (PCA)).

Results: MerCat2 allows for direct analysis of data properties in a database-independent manner that initializes all data, which other profilers and assembly-based methods cannot perform. MerCat2 represents an integrated tool to illuminate omics data within a sample for rapid cross-examination and comparisons.

Availability and implementation: MerCat2 is written in Python and distributed under a BSD-3 license. The source code of MerCat2 is freely available at https://github.com/raw-lab/mercat2. MerCat2 is compatible with Python 3 on Mac OS X and Linux. MerCat2 can also be easily installed using bioconda: mamba create -n mercat2 -c conda-forge -c bioconda mercat2.

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MerCat2：一种通用的 k-mer计数器和多样性估算器，用于从 omics 数据中获得与数据库无关的属性分析。

动机MerCat2（"Mer-Catenate2"）是一个多功能、并行、可扩展和模块化的属性软件包，用于对omics数据中的特征进行稳健分析。MerCat2 使用来自任何平台的大规模并行测序原始读数、组装 contigs 和蛋白质序列作为输入，执行任意长度 k 的 k-mer 计数，生成特征丰度计数表、质量控制报告、蛋白质特征度量和图形表示（即主成分分析 (PCA)）：结果：MerCat2 允许以独立于数据库的方式直接分析数据属性，并对所有数据进行初始化，这是其他剖析器和基于组装的方法无法做到的。MerCat2 是一种综合工具，可用于快速交叉检验和比较样本中的组学数据：MerCat2 由 Python 编写，采用 BSD-3 许可发布。MerCat2 的源代码可在 https://github.com/raw-lab/mercat2 免费获取。MerCat2 与 Mac OS X 和 Linux 上的 Python 3 兼容。使用 bioconda 也能轻松安装 MerCat2：mamba create -n mercat2 -c conda-forge -c bioconda mercat2。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量