bcftools: a set of companion tools, currently bundled with SAMtools, for identifying and filtering genomics variants.

bowtie: widely used, open source alignment software for aligning raw sequence reads to a reference genome.

BAM Format: binary, compressed format for storing SAM data.

BCF Format: Binary call format. Binary, compressed format for storing VCF data.

CIGAR String: Compact Idiosyncratic Gapped Alignment Report. A compact string that (partially) summarizes the alignment of a raw sequence read to the reference genome. Three core abbreviations are used: M for alignment match; I for insertion; and D for Deletion. For example, a CIGAR string of 5M2I63M indicates that the first 5 base pairs of the read align to the reference, followed by 2 base pairs, which are unique to the read, and not in the reference genome, followed by an additional 63 base pairs of alignment.

FASTA Format: text format for storing raw sequence data. For example, the FASTA file at: http://www.ncbi.nlm.nih.gov/nuccore/NC_008253 contains entire genome for Escherichia coli 536.

FASTQ Format: text format for storing raw sequence data along with quality scores for each base; usually generated by sequencing machines.

genotype likelihood: the probability that a specific genotype is present in the sample of interest. Genotype likelihoods are usually expressed as a Phred-scaled probability, where P = 10 ^ (-Q/10). For example, if the genotype TT (both alleles are T) at position 1,299,132 in human chromosome 12 (reference G) is 37, this translates to a probability of 10^-37/10 = 0.0001995, meaning that there is very low probability that the reads in your sample support a TT genotype. On the other hand, a genotype of AA at the same position with a score of 0 translates into a probability of 10^-0 = 1, indicating extremely high probability that your sample contains a homozygous mutation of G to A.

mate-pair: in paired-end sequencing, both ends of a single DNA or RNA fragment are sequenced, but the intermediate region is not. The two ends which are sequenced form a pair, and are frequently referred to as mate-pairs.

QNAME: unique identifier of a raw sequence read (also known as the Query Name). Used in FASTQ and SAM files.

paired-end sequencing: sequencing process where both ends of a single DNA or RNA fragment are sequenced, but the intermediate region is not. Particularly useful for identifying structural rearrangements, including gene fusions.

Phred-scaled probability: a scaled value (Q) used to compactly summarize a probability, where P = 10^-Q/10. For example, a Phred Q score of 10 translates to probability (P) = 10^-10/10 = 0.1. Phred-scaled probabilities are common in next-generation sequencing, and are used to represent multiple types of quality metrics, including quality of base calls, quality of mappings, and probabilities associated with specific genotypes. The name Phred refers to the original Phred base-calling software, which first used and developed the scale.

Phred quality score: a score assigned to each base within a sequence, quantifying the probability that the base was called incorrectly. Scores use a Phred-scaled probability metric. For example, a Phred Q score of 10 translates to P=10^-10/10 = 0.1, indicating that the base has a 0.1 probability of being incorrect. Higher Phred score correspond to higher accuracy. In the FASTQ format, Phred scores are represented as single ASCII letters. For details on translating between Phred scores and ASCII values, refer to Table 1 of this useful blog post from Damian Gregory Allis.

read-length: the number of base pairs that are sequenced in an individual sequence read.

read-depth: the number of sequence reads that pile up at the same genomic location. For example, 30X read-depth coverage indicates that the genomic location is covered by 30 independent sequencing reads. Increased read-depth translates into higher confidence for calling genomic variants.

RNAME: reference genome identifier (also known as the Reference Name). Within a SAM formatted file, the RNAME identifies the reference genome where the raw read aligns.

SAM Flag: a single integer value (e.g. 16), which encodes multiple elements of meta-data regarding a read and its alignment. Elements include: whether the read is one part of a paired-end read, whether the read aligns to the genome, and whether the read aligns to the forward or reverse strand of the genome. A useful online utility decodes a single SAM flag value into plain English.

SAM Format: Text file format for storing sequence alignments against a reference genome. See also BAM Format.

SAMtools: widely used, open source command line tool for manipulating SAM/BAM files. Includes options for converting, sorting, indexing and viewing SAM/BAM files. The SAMtools distribution also includes bcftools, a set of command line tools for identifying and filtering genomics variants. Created by Heng Li, currently of the Broad Institute.

single-read sequencing: sequencing process where only one end of a DNA or RNA fragment is sequenced. Contrast with paired-end sequencing.

VCF Format: Variant call format. Text file format for storing genomic variants, including single nucleotide polymorphisms, insertions, deletions and structural rearrangements. See also BCF format.

NextGenerationSequencing
A high-throughput sequencing method which parallelizes the sequencing process, producing thousands or millions of sequences at once.

DeepSequencing
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced.

Paired-EndSequencing
Sequence both ends of the same fragment and keep track of the paired data.

Adapter
Short oligonucleotides which are attached to the DNA to be sequenced. An adapter can provide a priming site for both amplification and sequencing of the adjoining, unknown nucleic acid.

Library
A collection of DNA fragments with adapters ligated to each end.

BridgeAmplification
Generation of in situ copies of a specific DNA molecule on an oligo-decorated solid support.

EmulsionPCR
A method for bead-based amplification of a library. A single adapter-bound fragment is attached to the surface of a bead, and an oil emulsion containing necessary amplification reagents is formed around the bead/fragment component. Parallel amplification of millions of beads with millions of single strand fragments produces a sequencer-ready library.

Alignment
Mapping of sequence reads to a known reference sequence

Referencesequence/genome 
A fully assembled version of a genome that can be used for mapping short DNA sequence reads for comparisons of genomes from various individuals

CoverageDepth
The number of nucleotides from reads that are mapped to a given position of reference genome.

Specificity 
The percentage of sequences that map to the intended targets out of total bases per run.

Uniformity 
The variability in sequence coverage across target regions.

Homopolymer
Uninterrupted stretch of a single nucleotide type (e.g., TTT or GGGGGG)

InDel
InDel stands for Insertion or deletion. A form of structural variation in which a DNA segment is either deleted or inserted.

SNP 

SNP stands for Single Nucleotide Polymorphism. A single base difference found when comparing the same DNA sequence from two different individuals.

Address of the bookmark: http://nemo2.sourceforge.net/index.html

Beagle version 4.1 has a more accurate genotype phasing algorithm and a very fast and accurate genotype imputation algorithm. Version 4.1 also has several changes to the command line arguments which are described in the release notes. The "ped" argument has no effect in version 4.1. If your data contains nuclear families and you want to model the parent-offspring relationships when phasing genotypes, please use version 4.0.

If you use Beagle 4.1 in a published analysis, please report the program version and cite the appropriate article.

The citation for Beagle's phasing algorithm is:

S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097.doi:10.1086/521987

The citation for Beagle's genotype imputation algorithm is:

B L Browning and S R Browning (2016). Genotype imputation with millions of reference samples. Am J Hum Genet 98:116-126.doi:10.1016/j.ajhg.2015.11.020

The citation for Beagle's IBD detection algorithm is:

B L Browning and S R Browning (2013). Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194(2):459-71.doi:10.1534/genetics.113.150029

Address of the bookmark: http://faculty.washington.edu/browning/beagle/beagle.html

http://compbio.cs.toronto.edu/prism/

Address of the bookmark: http://compbio.cs.toronto.edu/prism/

• Handle big sequence data, e.g:
  • Compare two vertebrate genomes
  • Align billions of DNA reads to a genome
• Indicate the reliability of each aligned column.
• Use sequence quality data properly.
• Compare DNA to proteins, with frameshifts.
• Compare PSSMs to sequences
• Calculate the likelihood of chance similarities between random sequences.
• Do split and spliced alignment.
• Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

Availability: YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA.

Contact:

http://genome.wustl.edu/people/groups/detail/hall-lab/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463118/

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

With Single Molecule, Real-Time (SMRT) Sequencing, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:

• Uncover missing heritability linked to structural variation
• Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease
• Resolve structural variation across the complete size spectrum with basepair resolution

Following are the SV tools, which can assist you to achieve your goal.

Sniffles: Structural variation caller using third generation sequencing

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled! 

More at https://github.com/fritzsedlazeck/Sniffles

MultiBreak-SV: It identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

There are two pieces of software in this release: (1) a pre-processor that takes machineformat (.m5) BLASR files, and (2) MultiBreak-SV. For installation and usage instructions, see doc/MultiBreakSV-Manual.txt.

More at https://github.com/raphael-group/multibreak-sv

Parliament: A Structural Variation Tool. Why ask a single sv-detection approach to find every variant when you can have a parliament of tools deciding?

Publication about the algorithm and “…the first long-read characterization of structural variation in a diploid human personal genome…” (HS1011) - “Assessing structural variation in a personal genome—towards a human reference diploid genome”

More at https://sourceforge.net/projects/parliamentsv/

https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf

PBHoney: the structural variation discovery tool 

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract

More at https://sourceforge.net/projects/pb-jelly/

SMRT-SV: Structural variant and indel caller for PacBio reads

Structural variant (SV) and indel caller for PacBio reads based on methods from Chaisson et al. 2014.

SMRT-SV provides an official software package for tools described in Chaisson et al. 2014 and adds several key features including the following.

• Unified variant calling user interface with built-in cluster compute support
• Small indel calling (2-49 bp)
• Improved inversion calling (screenInversions)
• Quality metric for SV calls based on number of local assemblies supporting each call
• Higher sensitivity for SV calls using tiled local assemblies across the entire genome instead of "signature" regions
• Genotyping of SVs with Illumina paired-end reads from WGS samples

More at https://github.com/EichlerLab/pacbio_variant_caller

It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the de facto standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer.^[1]

Address of the bookmark: https://en.wikipedia.org/wiki/FASTQ_format