Trimmomatic is a read trimming tool for Illumina NGS data [1]. It is a flexible tool providing several functions to be operated on reads. These functions include trailing, leading, and several other quality control operations. In this article, we are going to perform trailing on NGS paired-end reads data using the GALAXY platform [2]. (more…)

Bismark is bioinformatics to map bisulfite treated sequencing reads and to perform methylation calls [1]. In this article, we are going to extract methylation information from Bismark alignment outputs. (more…)

Bismark is a bioinformatics tool to map bisulfite treated sequencing reads to a genome [1]. It also determines cytosine methylation sites. In this article, we will install Bismark on Ubuntu. (more…)

We use somatic variant callers to detect mutations in cancer samples by comparing sequencing data tumor and normal sample pairs. This is followed by some ad-hoc filtering that may produce low precision data resulting in a large number of false positives. (more…)

One of the major next-generation sequencing (NGS) technologies that are most frequently used in medical research is Ion Torrent. Software for Ion Torrent machines provides output in BAM files that are huge in size. Additionally, their compression is also space expensive. (more…)

Transcriptome represents the complete set of all expressed transcripts (RNA molecules) present in a cell or tissue at a given point of time. The transcriptome is always dynamic in nature and keeps on changing with time driven by the external and internal environment. (more…)

What is predictive metagenomics profiling?

Recently, predictive metagenomics profiling (PMP) has been added to the microbial ecologist’s arsenal of strategies for probing microbial communities. (more…)

High throughput sequencing has revolutionized the new world of bioinformatics research. Since everyone is aware of the Human Genome project in which the human genome has been sequenced, millions of species have been sequenced so far. Sequencing is a very important aspect of bioinformatics so new faster and better sequencing techniques are needed . New sequencing platforms produce biological sequence fragments faster and cheaper.

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