A curated list of NGS tools mentioned in our chapter, including tool names and their official links. This repository serves as a quick reference for readers and researchers.
General NGS Data Analysis
FastQC – Quality control for high throughput sequence data https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
MultiQC – Aggregate QC reports from multiple tools https://multiqc.info/
Trimmomatic – Read trimming and filtering http://www.usadellab.org/cms/?page=trimmomatic
Cutadapt – Adapter trimming https://cutadapt.readthedocs.io/en/stable/
Fastp – Fast and all-in-one preprocessor for FASTQ files https://github.com/OpenGene/fastp
Read Alignment
BWA – Burrows-Wheeler Aligner http://bio-bwa.sourceforge.net/
Bowtie2 – Ultrafast and memory-efficient tool for aligning sequencing reads http://bowtie-bio.sourceforge.net/bowtie2/
STAR – Spliced Transcripts Alignment to a Reference (RNA-seq) https://github.com/alexdobin/STAR
HISAT2 – Fast and sensitive alignment of NGS reads https://daehwankimlab.github.io/hisat2/
Post-alignment Processing
SAMtools – Tools for manipulating alignments in SAM/BAM format http://www.htslib.org/
Picard – A set of Java command-line tools for manipulating high-throughput sequencing data https://broadinstitute.github.io/picard/
GATK – Genome Analysis Toolkit (variant discovery) https://gatk.broadinstitute.org/
Transcriptomics/RNA-seq
HTSeq – Python framework for counting aligned reads https://htseq.readthedocs.io/en/master/
featureCounts (Subread) – Assigns reads to genomic features http://bioinf.wehi.edu.au/featureCounts/
DESeq2 – Differential expression analysis based on the negative binomial distribution https://bioconductor.org/packages/release/bioc/html/DESeq2.html
edgeR – Empirical analysis of digital gene expression data https://bioconductor.org/packages/release/bioc/html/edgeR.html
CRISPR Screen Analysis
MAGeCK – Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout https://sourceforge.net/p/mageck/wiki/Home/
CRISPResso – Analysis of genome editing outcomes https://crispresso.pinellolab.partners.org/
PinAPL-Py – CRISPR pooled screen analysis pipeline https://pinapl-py.readthedocs.io/en/latest/
JACKS – Joint Analysis of CRISPR/Cas9 Knockout Screens https://github.com/felicityallen/JACKS
ChIP-seq / ATAC-seq
MACS2 – Model-based Analysis for ChIP-Seq https://github.com/macs3-project/MACS
HOMER – Motif discovery and next-gen sequencing analysis http://homer.ucsd.edu/homer/