Bioinformatics Tools

A collection of commonly used bioinformatics tools for sequencing data analysis.

Cutadapt - Remove adapter sequences and trim low-quality bases from sequencing reads
BWA-MEM - Fast DNA sequence aligner for Illumina reads using Burrows-Wheeler Transform
Bowtie2 - Ultrafast memory-efficient aligner for short DNA sequences, ideal for ChIP-seq and ATAC-seq
STAR - Spliced RNA-seq aligner for detecting splice junctions and gene fusions
iVar - Primer trimming and variant calling for amplicon-based viral sequencing data
miRDeep2 - Identify and quantify known and novel microRNAs from small RNA-seq data

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title: "Bioinformatics Tools"
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A collection of commonly used bioinformatics tools for sequencing data analysis.

- [**Cutadapt**](cutadapt.qmd) - Remove adapter sequences and trim low-quality bases from sequencing reads

- [**BWA-MEM**](bwa-mem.qmd) - Fast DNA sequence aligner for Illumina reads using Burrows-Wheeler Transform

- [**Bowtie2**](bowtie2.qmd) - Ultrafast memory-efficient aligner for short DNA sequences, ideal for ChIP-seq and ATAC-seq

- [**STAR**](star.qmd) - Spliced RNA-seq aligner for detecting splice junctions and gene fusions

- [**iVar**](ivar.qmd) - Primer trimming and variant calling for amplicon-based viral sequencing data

- [**miRDeep2**](mirdeep2.qmd) - Identify and quantify known and novel microRNAs from small RNA-seq data