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Bioinformatics Scripts
Command-line examples for common FASTQ, FASTA, SAM, BED, alignment, and quantification tasks in Linux.
- FASTQ quality control and trimming
- FASTA reference preparation
- Read alignment and raw-count generation
Resources
Bioinformatics scripts, tutorials, and learning materials for sequencing data analysis.
Explore SciBerg resources for Linux-based bioinformatics workflows, NGS data processing, FASTQ/FASTA manipulation, read alignment, raw-count generation, molecular biology fundamentals, and practical data-analysis training.
Resource library
Start with scripts, tutorials, or molecular biology foundations.
The current resource library is organized into practical Linux bioinformatics scripts, an NGS data analysis tutorial outline, and a molecular biology course outline.
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NGS Data Analysis Tutorial
A structured outline for learning NGS data analysis, from Linux setup to DNA-seq, RNA-seq, bisulfite-seq, ChIP-seq, and metagenomics.
- Linux and command-line basics
- Data formats and quality control
- Core NGS analysis workflows
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Molecular Biology Course
A course outline covering nucleic acids, proteins, transcription, translation, replication, genome structure, and genome instability.
- Nucleic acids and proteins
- Transcription and translation
- DNA replication and genome biology
Bioinformatics scripts
Practical Linux examples for common NGS preprocessing and analysis steps.
These resources help users perform basic command-line operations that frequently appear in sequencing-data workflows.
Primary analysis of FASTQ files
Initial FASTQ quality checks and FastQC-style reports.
Open →Trimming and filtering of NGS reads
Adapter trimming and read filtering workflows.
Open →Removing duplicated sequences from FASTA files
Cleaning reference FASTA files before downstream analysis.
Open →Extracting specific sequences from FASTA files
Selecting sequences by header IDs or sequence lists.
Open →Preparing FASTA references for RNA classes
Creating RNA-class-specific references from transcriptome FASTAs.
Open →Manipulation with FASTA and FASTQ files in Linux
Basic command-line operations for FASTA and FASTQ files.
Open →Converting GTF files into BED files
Transforming genome annotation formats for interval workflows.
Open →Extracting promoter and TSS sequences
Generating promoter or TSS FASTA files from genome references.
Open →Reads alignment with Bowtie, Bowtie2, BWA, HISAT, and STAR
Examples for mapping sequencing reads to reference sequences.
Open →Manipulations with SAM files
Basic SAM-file operations for alignment-derived outputs.
Open →Calculate raw read counts with eXpress and RSEM
Raw-count generation and transcript quantification examples.
Open →
Practical learning
Resources designed for scientists working with real sequencing data.
The resources bridge the gap between biological questions and practical command-line data processing. For project-specific support, SciBerg can provide custom NGS analysis, clinical bioinformatics, and AI-enabled workflow development.
For wet-lab scientists
Understand core NGS data-processing concepts and what happens after sequencing data are delivered.
For bioinformatics beginners
Learn Linux-based analysis steps through concrete examples for common file formats and tools.
For collaborators and partners
Use the resource library to clarify workflows, expected deliverables, and project-specific analysis needs.
For AI-enabled workflows
Contact SciBerg to integrate automated reporting, literature-context summaries, or private research assistants into your analysis process.
Tutorial outlines
Structured learning paths for NGS and molecular biology.
These pages provide learning outlines that can be expanded into lectures, tutorials, hands-on workshops, or internal training material.
NGS Data Analysis Tutorial
Core topics for learning how to set up and perform basic NGS data-analysis workflows.
- Ubuntu/Linux setup and software installation
- Unix command line and custom scripting
- Data sources, data formats, and QC
- Short-read alignment
- DNA-seq, RNA-seq, bisulfite-seq, ChIP-seq, and metagenomics
Open NGS Tutorial
Molecular Biology Course
Foundational molecular biology topics relevant to sequencing, gene regulation, and genome analysis.
- Structure of nucleic acids and proteins
- Genetic code, transcription, and translation
- mRNA processing and regulation
- DNA replication, DNA repair, and genome topology
- Genome structure, gene classification, and genome instability
Open Molecular Biology Course
Need project-specific support?
Contact SciBerg
Turn learning resources into a reproducible analysis workflow for your data.
SciBerg can help with NGS data analysis, clinical bioinformatics, custom pipelines, automated reporting, and AI integration for academic, clinical, biotech, and industrial partners.