GenomeSyn

Variation:

SnpEff- Genomic variant annotations and functional effect prediction toolbox.

Annovar- An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. 

Ensembl Variant Effect Predictor (VEP)- A powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions.

Oncotator- A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers.

NextSV- An automated pipeline for structrual variation detection from long-read sequencing.

Manta- Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. 

Read mapping:

Minimap2- A versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

Bowtie2- An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

BWA- A software package for mapping low-divergent sequences against a large reference genome.

BWA MEM- A software package for mapping low-divergent sequences against a large reference genome.

HISAT2- A fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

VG map- For working with genome variation graphs.

GraphAligner- A tool for aligning long reads to sequence graphs.

Minigraph- A sequence-to-graph mapper and graphconstructor. 

Giraffe- A functional ASP.NET Core micro web framework for building rich web applications.

Single-nucleotide variant (SNV) genotyping:

GATK- Variant discovery in high-throughput sequencing data.

FreeBayes- Bayesian haplotype-based genetic polymorphism discovery and genotyping.

bcftools- Utilities for variant calling and manipulating VCFs and BCFs.

Structural variation (SV) genotyping:

Svtyper- A Bayesian genotyper for structural variants.

SVJedi- Genotyping structural variations with long reads.

Sniffles- Used to detect SV of long read data.

Gene annotation:

MAKER2- An annotation pipeline and genome-database management tool for second-generation genome projects.

Funannotate- A genome prediction, annotation, and comparison software package.

BRAKER2- Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.

Homology searches:

BLAST- Basic local alignment search tool.

DIAMOND- Accelerated BLAST compatible local sequence aligner.

HMMER- Used for searching sequence databases for sequence homologs, and for making sequence alignments.

ChIP-seq peak calling:

MACS- Model-based Analysis for ChIP-Seq.

Transcript mapping and quantification:

HISAT2- A fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

STAR- RAN-seq aligner.

Kallisto- A program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

featureCounts- A ultrafast and accurate read summarization program.

RSEM- Accurate transcript quantification from RNA-Seq data with or without a reference genome.

Visualization:

MUMmer- A system for rapidly aligning large DNA sequences to one another.

GBrowse- A combination of database and interactive web pages for manipulating and displaying annotations on genomes.

JBrowse- The next generation genome browser.

IGV- Embeddable genomic visualization component based on the Integrative Genomics Viewer.