Tools

Choosing the right tools for NGS (Next-Generation Sequencing) analysis involves several key considerations:

Define Your Goals: Clearly outline your objectives (e.g., variant calling, transcriptome analysis, metagenomics) to narrow down suitable tools.
Data Type: Consider the type of NGS data you have (e.g., DNA-seq, RNA-seq, ChIP-seq) as tools are often optimized for specific data types.
Scalability: Ensure the tools can handle your data size. Some tools are better suited for large datasets or high-throughput analyses.
Accuracy and Reliability: Look for tools with proven performance and community support. Check published studies or benchmarks for validation.
User-Friendly Interface: If you’re not very experienced, opt for tools with graphical user interfaces (GUIs) or comprehensive documentation.
Integration with Other Tools: Consider tools that can integrate well with existing pipelines or workflows, particularly in a bioinformatics framework.
Community and Support: Active user communities and available support can be invaluable for troubleshooting and learning.
Cost and Licensing: Assess whether the tools are open-source or require licensing fees, as budget constraints can influence your choice.
Computational Requirements: Evaluate the hardware requirements and whether you have the necessary computational resources available.
Reproducibility: Opt for tools that support reproducible research practices, allowing for easier sharing and validation of results.

single nucleotide variant calling

Name	Published	Control Needed	Indel Detection	Contamination Correction	Ref
Varscan2	2012	+	+	−	1
MuTect2 *	2013	+	−	+	2
FreeBayes	2012	−	+	−	3
Strelka *	2012	+	+	−	4
Platypus *	2014	−	+	−	5
SomaticSniper *	2012	+	−	−	6
LoFreq *	2012	−	+	+	7
VarDict *	2016	−	+	−	8
JointSNVMix *	2012	+	−	−	9
MutationSeq *	2012	+	−	−	10
EBCall *	2013	+	+	−	11
MuSE *	2016	+	−	+	12
RADIA	2014	+	−	+	13
Virmid	2013	+	−	+	14
deepSNV *	2014	+	−	−	15
Shimmer *	2013	+	−	+	16
qSNP *	2013	+	−	+	17
BAYSIC	2014	+	−	−	18
SomaticSeq *	2015	+	+	−	19
CaVEMan *	2016	+	−	+	20
SNooPer *	2016	−	+	+	21
SNVSniffer *	2016	−	+	−	22
HapMuC	2014	−	+	−	23
FaSD-somatic	2014	−	−	−	24
LocHap *	2016	+	+	+	25
LoLoPicker *	2017	+	−	+	26

Copy Number Variations

Name	Published	Control Needed	Contamination Correction	GC-Content Correction	REF
Varscan2	2012	+	−	−	1
CNVnator	2011	+	−	+	2
CNV-Seq	2009	+	−	−	3
CoNIFER	2012	−	+	−	4
Control-FREEC	2012	−	+	+	5
ExomeCNV	2011	+	+	−	6
XHMM	2012	−	+	+	7
ExomeDepth	2012	+	−	+	8
cn.MOPS	2012	−	+	+	9
Cnvkit	2016	+	+	+	10
CONTRA	2012	−	−	+	12
Sequenza	2015	+	−	+	13
EXCAVATOR	2013	+	+	+	14
CODEX	2015	−	+	+	16
ADTEx	2014	+	−	+	17
Seqgene	2011	+	−	−	18
FishingCNV	2013	−	−	−	19
HMZDelFinder	2017	−	−	−	20
ExoCNVTest	2012	+	−	−	21
CLAMMS	2016	−	−	+	22
falcon	2015	+	+	−	23
saasCNV	2015	+	+	−	24
WISExome	2017	−	−	−	25
GATK

Structural Variations

Name	Description	REF
Manta	Manta is a structural variant caller developed by Illumina. It detects various types of SVs, including deletions, duplications, inversions, and translocations. Works with whole-genome and exome sequencing data.	1
Delly	Delly is a versatile SV detection tool that can identify deletions, duplications, inversions, translocations, and more. It works with various sequencing data types, including exome data.	2
Lumpy	Lumpy focuses on identifying interchromosomal translocations and intrachromosomal rearrangements. It can be adapted for use with exome data.	3
BreakDancer	Pindel detects breakpoints of large deletions, medium-sized insertions, inversions, tandem duplications, and other structural variants. Suitable for both whole-genome and exome data.	4
GRIDSS	GRIDSS is a versatile SV caller that can detect complex structural variants by combining multiple evidence types. Suitable for various sequencing data types, including exome data.	5
CNVkit	CNVkit is primarily for copy number variation detection but can also identify large-scale structural variations from exome data by analyzing read depth.	6
TIDDIT	TIDDIT is designed for identifying tandem duplications and can be used with exome sequencing data to detect this specific type of structural variation.	7

Splicing Site Detection

Name	Description	REF
SpliceAI	SpliceAI is a deep learning-based tool that predicts the effect of variants on splicing, providing information about splice site alterations.	1
Human Splicing Finder (HSF)	HSF is a web-based tool that predicts the potential impact of variants on splicing, analyzing consensus splice site sequences for potential disruptions.	2
MMSplice	MMSplice is a machine learning-based tool that predicts the impact of variants on alternative splicing events, providing a score for splicing disruption likelihood.	3
SplicePort	SplicePort is a web-based tool that predicts the potential impact of variants on splice site creation or disruption, considering both donor and acceptor splice sites.	4

Annotation

Name	Description	REF
Annovar	ANNOVAR is a versatile tool for annotating genetic variants, providing information on variant function, population allele frequencies, and predicted functional consequences.	1
SnpEff	SnpEff annotates genetic variants, categorizing them based on functional impact and providing annotations on genes and transcripts.	2
dbNSFP	The Database for Non-Synonymous SNPs' Functional Predictions (dbNSFP) provides functional predictions for non-synonymous variants in exomes, including predictions from multiple tools.	3
Exomiser	Exomiser prioritizes and annotates variants in exome data for rare disease research, integrating variant data with various databases and gene-phenotype information.	4
VCFanno	VCFanno is a flexible tool for annotating VCF files, allowing customization of annotation sources and rules.	5
VEP	VEP is a powerful tool from Ensembl for annotating genetic variants, offering insights into functional effects, gene impacts, regulatory regions, and population allele frequencies.	6
VariantDB	VariantDB is a platform for variant annotation and interpretation, providing various annotation sources and custom annotation tracks.	7
GnomAD	The Genome Aggregation Database (gnomAD) offers access to allele frequencies of genetic variants in large populations, useful for annotating exome variants.	8
ClinVar	ClinVar is a database of clinically relevant variants, providing annotations related to clinical significance and associations with diseases.	9
OMIM	OMIM is a comprehensive database of genetic disorders and associated genes, useful for annotating exome variants with disease-related information.	10