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a computer screen with a bunch of data on it

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Building a bioinformatics pipeline

Databases

EMBL
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black blue and yellow textile

A comprehensive database for nucleotide sequences

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a man riding a skateboard down the side of a ramp
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a man riding a skateboard down a street next to tall buildings
GenBank

An annotated collection of publicly available DNA sequences from various organisms

A curated database of protein sequences and functional information

UniPort
GATK
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black blue and yellow textile

A quality control tool that provides a visual summary of high-throughput sequencing data to identify potential issues.

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a man riding a skateboard down the side of a ramp
a man riding a skateboard down a street next to tall buildings
a man riding a skateboard down a street next to tall buildings
MultiQC

Aggregates results from multiple bioinformatics tools (like FASTQC) into a single comprehensive report for easier analysis.

A base-calling program that assigns quality scores to DNA sequencing reads, indicating the accuracy of each base call.

FastQC
Phred

Data Acquisition and Quality Control

BWA / Bowtie2
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black blue and yellow textile

Efficient aligners for mapping sequencing reads to reference genomes

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a man riding a skateboard down the side of a ramp
a man riding a skateboard down a street next to tall buildings
a man riding a skateboard down a street next to tall buildings
HISAT2

A fast and sensitive tool for aligning RNA-seq reads

A high-performance aligner designed for RNA-seq data

STAR

Read Alignment / Mapping

Picard
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A set of command‑line utilities for manipulating high‑throughput sequencing data (BAM/SAM)

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a man riding a skateboard down the side of a ramp
a man riding a skateboard down a street next to tall buildings
a man riding a skateboard down a street next to tall buildings

Sambamba

Fast and efficient BAM/SAM file processing—covering indexing, sorting, and more

Essential utilities for working with SAM and BAM data formats

SAMtools

Post-Alignment Processing

GATK
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black blue and yellow textile

At toolkit for variant discovery in high-throughput sequencing data focused on post-alignment processing such as base recalibration and variant calling

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a man riding a skateboard down the side of a ramp
a man riding a skateboard down a street next to tall buildings
a man riding a skateboard down a street next to tall buildings
HTseq

A python package for counting reads aligned to genomic features

Toos for peak calling (MASC2) and deep-sequencing data analyzing (deepTools)

MACS2 / deepTools

Variant Calling or Quantification

Bioconductor
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black blue and yellow textile

An open‑source project that offers extensive tools for genomic data analysis in R

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a man riding a skateboard down the side of a ramp
a man riding a skateboard down a street next to tall buildings
a man riding a skateboard down a street next to tall buildings
DESeq2

An R package for differential expression analysis of RNA‑seq data

An R package for differential expression analysis of RNA‑seq data

edgeR

Statistical Analysis and Biological Interpretation