Performs short read alignment using the Burrows-Wheeler index in order to be memory efficient, while still maintaining an alignment speed of over 25 million 35 bp reads per hour.
Performs short and long read alignment, detects long and short distance splicing, SNPs, and is capable of detecting bisulfite-treated DNA for methylation studies.
Short read aligner compatible with Illumina-Solexa and ABI SOLiD data, performs ungapped alignment allowing 2-3 mismatches for single-end reads and one mismatch for paired-end reads.
Performs short read alignment allowing for INDELs up to 8 bp, for Illumina generated data. Paired-end mapping using a one end anchored algorithm allows for detection of novel insertions.
Alignment done on paired-end or single-end sequences, also capable of doing methylation studies. Allows for a mismatch up to 50% of a read length and has built-in adapter and base quality trimming.
SOAP2 improved speed by an order of magnitude over SOAP1 and can align a wide range of read lengths at the speed of 2 minutes for one million single-end reads using a two-way BWT algorithm.
Alignment done using a hashing algorithm and statistical model, to align Illumina reads for genome, RNA, and Chip sequencing allowing for a large number or variations including insertions and deletions.
Uses a 0() algorithm that uses both hash and tri-based methods that are effective in aligning sequences over 200 bp with 3 times less memory and ten times faster than SSAHA.
Detection of SNPs, MNPs, INDELs, replacements, and structural variants (SVs) from sequencing alignments using local realignment and local assembly to achieve high specificity and sensitivity.
Part of the NHBLI sequencing project; this database contains novel and known SNVs and INDELs including accession number, function of the variant, and HapMap frequencies, clinical association, and PolyPhen predictions.
Machine learning algorithm to score all possible 8.6 million substitutions in the human reference genome from 1 to 99 based on known and simulated functional variants.
Uses the Likelihood Ratio statistical test to compare a variant to known variants and determine if they are predicted to be benign, deleterious, or unknown.
Using two bam files as input, this tool uses the genotype likelihood model of MAZ to calculate the probability that the tumor and normal samples are different, thus identifying somatic variants.
Detects copy number changes and loss of heterozygosity (LOH) from paired SAM/BAM files by computing and normalizing copy number and beta allele frequency.
Gene-specific and patient-specific mutation frequencies are incorporated to find mutations in genes that are mutated more often than would be expected by chance.
Allows for users to input a large set of genes and discover the functional annotation of the gene list including pathways, gene ontology terms, and more.
Tools and resources for linking variants to therapeutics
cBioPortal
Database that allows the download, analysis, and visualization of cancer sequencing studies, including providing patient and clinical data for samples.
Database of relationship between phenotypes and human variations, showing the relationship between health status and human variations and known implications.
Database of drug signatures that includes 19,531 genes and 17,389 compounds that can in part help identify compounds for drug repurposing studies in translational research.
Whole Exome Sequencing pipeline that starts with raw sequencing (fastq) files and ends with a VCF file that has good capability for novel and expert users.
WES or WGS pipeline that combines the information from over ten alignment and analysis tools to arrive at a VCF file that can be used in both Mendelian and cancer studies.
WES data analysis pipeline that starts with raw sequencing reads and analyzes SNVs and CNAs and links this data to a list of prioritized drugs from clinical trials and DSigDB.
Automated sequencing pipeline that performs in part alignment, variant calling, and quality control that can be run on Amazon Web Services EC2 as well as local machines and clusters.
