SNP/SNV annotation software tools | High-throughput sequencing data analysis
The latest sequencing instruments in conjunction with SNP discovery tools can be used to identify huge numbers of putative SNPs. Whether the SNPs are discovered through genome or transcriptome sequencing the next problem after identification is often annotating and choosing functionally important SNPs.
An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day.
Corrects draft assemblies and calls sequence variants of multiple sizes, including very large insertions and deletions. Pilon improves draft genome assemblies by correcting bases, fixing miss-assemblies and filling gaps. In addition, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions.
Assists users to visualize, identify and annotate prophage sequences within bacterial genomes or plasmids. PHAge Search Tool performs identification using either raw or annotated bacterial genome sequence data. The main features are: (1) prophage region identification support for both raw nucleotide sequence input; (2) support for detailed prophage annotation including position, length, boundaries, number of genes, and attachment sites; and (3) support for the prediction of the completeness or potential viability of identified prophages.
Annotates and predicts the effects of single nucleotide polymorphisms (SNPs). SnpEff features include: (1) the ability to make thousands of predictions per second; (2) the ability to add custom genomes and annotations; (3) the ability to integrate with Galaxy (4) compatibility with multiple species and multiple codon usage tables, (5) integration with Broad's Genome Analysis Toolkit (GATK) and (6) the ability to perform non-coding annotations. It enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.
Allows users to process biological sequencing data. ea-utils works with pipeline based on Illumina and can run with other FASTQs. It offers several functions such as scanning a sequence file for adapters to determine a set of clipping parameters and perform clipping. It can demultiplex FASTQ files and can check if the reads are in-sync during the demultiplexing.
Allows detection of genetic variants that uses Next Generation Sequencing (NGS) data. Variant Calling Pipeline can annotate these data, but can also threat single nucleotide polymorphisms (SNPs) according to a given reference sequence.
Assists in selecting functionally relevant single nucleotide polymorphisms (SNPs) for large-scale genotyping studies of multifactorial disorders. SNPnexus allows researchers to assess the potential significance of candidate sequence variants and points to the altered gene/protein isoforms that may lead to phenotypic changes. It also allows single queries using dbSNP identifiers or chromosomal regions for annotating known variants.