Software
SequelTools: A new suite for PacBio Sequel raw sequence data analysis
A new suite of tools called SequelTools has been developed for analyzing PacBio raw sequence data [1]. Pacbio is a third-generation DNA sequencing method that is capable of detecting methylated bases, gives very long reads, and provides real-time sequencing.
SequelTools is a command-line program that consists of tools for read subsampling, quality control, and read filtering [1]. According to the authors, there is no such tool available yet for analyzing the quality, subsampling, and filtering of PacBio raw sequence data.
SequelTools consists of three tools that can be used one at a time.
1. Quality Control (QC) tool
This tool processes SMRTcells and generates multiple statistics and plots. These plots describe the quality of input data.
2. Read subsampling tool
It subsamples reads based on different criteria selected by the user such as random CLR selection or longest subreads per CLR.
3. Read filtering tool
This tool allows users to normalize data by minimum length or by filtering out certain low-quality scrap reads.
These tools can be easily used with command-line arguments. The main script written in bash uses Samtools for file conversion BAM and SAM file formats.
SequelTools is developed in R, bash, and Python. It requires BAM format files as input. The suite is freely accessible, fast, and efficient, and is available at https://github.com/ISUgenomics/SequelTools. It can be run on any operating system. The performance of SequelTools was also tested on benchmark data. It revealed that SequelTools took around half an hour while processing scraps only and a little more than an hour with scraps and subreads [1].
For further details, read here.
References
- Hufnagel, D. E., Hufford, M. B., & Seetharam, A. S. (2020). SequelTools: a suite of tools for working with PacBio Sequel raw sequence data. BMC bioinformatics, 21(1), 1-11.
Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.
Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].
AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)
Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.
PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)
While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.
Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)
In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)
SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization [1]. In this article, we are going to install SMINA on Ubuntu (Linux). (more…)
ClusCo is a bioinformatics software to perform clustering and comparison of protein models [1]. In this article, we are going to install ClusCo on Ubuntu (Linux). (more…)
Running a plugin on an old version of Pymol [1] can give you multiple errors that are not easy to troubleshoot. For example, LigAlign plugin [2] runs on an old version of Pymol. Previously, we explained how to install LigAlign on Pymol. In this article, we will run the LigAlign command on Pymol. (more…)
Few errors appear when we try to run the LigAlign plugin [1] in Pymol [2]. For example, if you try to run the ligand_alignment plugin, it will give you multiple errors including “Unable to initialize LigAlign v1.00“, or “can’t run LigAlign v1.00” or “incorrect Python syntax” or “Plugin has been installed but initialization failed“. In this article, we explain the reason for this issue and how you can rectify these errors. (more…)
Sometimes we need to access old versions of Pymol [1]. Running some plugins on Pymol is difficult due to Python incompatibility. New Pymol versions require Python 3.x whereas older versions run on Python 2.x. Therefore, we need to maintain multiple versions of Pymol on a single system. In this article, we will install Pymol 1.7.x along with the latest version (Pymol 2.5.2) on Ubuntu. Later, we will create shortcuts for them.
Previously, we provided a tutorial for Pymol installation on Ubuntu. In this article, we are going to install Pymol on Mac OS. (more…)
In this article, we are going to install VMD [1] on Ubuntu. (more…)
We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS. (more…)
PyMol is one of the most widely used bioinformatics software. Generally, it is used as a molecular viewer to visualize macromolecules and small molecules. In this article, we are discussing several uses and applications of PyMol. (more…)
You must be logged in to post a comment Login