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Software Tools For NGS Read Alignment & Reference Mapping


Complex Analysis Workflow | Quality Control & Data Trimming | Assembling & Binning | Alignment & Mapping | Data Analysis | Variant Analysis & Variant Calling | Data Bases & Data Base Search | Visualisation


Alignment & Reference Mapping | Genetic Linkage Mapping


NGS Read Alignment and Reference Mapping Software

Align2rawsignal

Align2rawsignal (aka. WIGGLER. because it generates wiggle files) reads in a set of tagAlign/BAM files, filters out multi-mapping tags and creates a consolidated genome-wide signal file using various tag-shift and smoothing parameters as well as various normalization schemes.
Source: Code Google

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BFAST

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.
Source: Sourceforge

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BLASR

BLASR The PacBio® long read aligner

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Burrows-Wheeler Aligner (BWA)

BWA Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome.
Source: Sourceforge

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Bowtie

Bowtie is an ultrafast, memory-efficient short read aligner. It indexes the genome with a Burrows-Wheeler index to keep its memory footprint small.
Source: Sourceforge

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Blast

Blast Local alignment search tool

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BLAT

BLAT (DNA alignment tools)

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CRISPRAlign

CRISPRAlign E-CRISP has been optimized using fast and accurate algorithms to design CRISPR gRNA sequences to target any nucleotide sequence ranging from single exons to entire genomes. Special emphasis in the design process has been given to usability in experimental applications. E-CRISP not only checks for target specificity of the putative designs but also assesses their genomic context (e.g. exons, transcripts, CpG islands.
Source: Omics

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FusionMap

FusionMap is an efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies.
Source: Array Server

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GENALICE MAP

GENALICE MAP is a Next-Generation alignment solution that deals with all. GENALICE MAP preprocesses your data on standard dual processor hardware. Faster, better and extremely cost-effective.
Source: Genalice

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GMAP

GMAP A Genomic Mapping and Alignment Program for mRNA and EST Sequences.

Source: Research Pub

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gsMapper

Reference-guided alignment and variation detection for resequencing projects
Source: 454

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GSNAP

GSNAP is a Genomic Short-read Nucleotide Alignment Program. The tool incorporated SNP information into mapping and supports splicing while performing the mapping. 

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HISAT

HISAT is a fast and sensitive spliced alignment program. As part of HISAT, we have developed a new indexing scheme based on the Burrows-Wheeler transform (BWT) and the FM index, called hierarchical indexing, that employs two types of indexes: (1) one global FM index representing the whole genome, and (2) many separate local FM indexes for small regions collectively covering the genome.
Source: John Hopkin University

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HiSeq Analysis Software (HAS)

HiSeq Analysis Software (HAS) is a software package for processing sequencing results generated by Illumina HiSeq sequencers. HiSeq Analysis Software performs secondary analysis on the base calls and quality scores in bcl files generated on-instrument by the RTA software. HiSeq Analysis Software produces information about alignment, variants, or other analysis results for each sample in an analysis.
Source: Illumina

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LAST

LAST is a sequence alignment software (for long reads PacBio).

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MapSplice

MapSplice enables accurate mapping of RNA-seq reads for splice junction discovery

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Maq

Maq first aligns reads to reference sequences and then calls the consensus. At the mapping stage, maq performs ungapped alignment. For single-end reads, maq is able to find all hits with up to 2 or 3 mismatches, depending on a command-line option; for paired-end reads, it always finds all paired hits with one of the two reads containing up to 1 mismatch.
Source: Sourceforge

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mrsFAST

mrsFAST is designed to map short reads to reference genome assemblies; in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that optimizes cache usage to get higher performance.
Source: GitHub

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MUSCLE

MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.

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MOSAIK

MOSAIK is a reference-guided aligner for next-generation sequencing technologies.

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metaCRT

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NovoAlign

NovoAlign is a Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms.

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Partial-order alignment (POA) software

POA is Partial Order Alignment, a fast program for multiple sequence alignment in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment.
Source: Sorceforge

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PASS

PASS has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments.
Source: University de Padova

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PyNAST

PyNAST is a reimplementation of the NAST sequence aligner, which has become a popular tool for adding new 16s rRNA sequences to existing 16s rRNA alignments. This reimplementation is more flexible, faster, and easier to install and maintain than the original NAST implementation. PyNAST is built using the PyCogent Bioinformatics Toolkit (PyCogent.
Source: BioCore

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RAPSearch2

RAPSearch2 is a tool for fast protein similarity searches. RAPSearch2 searches short DNA sequences (reads) or protein sequences against protein database, achieving >100times speedup as compared to BLASTX (for reads of ~100bp), or >1000 times speedup over BLASTX in the accelerating mode (option "-a"). RAPSearch2 utilizes reduced amino acid alphabet and flexible seed so that seeds of various lengths with mismatches can be identified quickly by hashing.
Source: Sourceforge

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RazerS

RazerS is a read mapping program with adjustable sensitivity based on counting q-grams. In this work we propose the successor RazerS 3 which now supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers’ bit-vector algorithm for verification, memory saving measures and support for the SAM output format.
Source: SEQAN

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RMAP

RMAP is aimed to map accurately reads from the next-generation sequencing technology. RMAP can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.
Source: Cold Spring Harbor Laboratory

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RUM

RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.RUM can also be used effectively for DNA sequencing (e.g. ChIP-Seq) and microarray probe mapping.
Source: Github

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SARUMAN (Semiglobal Alignment of Short Reads using CUDA and Needleman-Wunsch)

The result is SARUMAN (Semiglobal Alignment of Short Reads using CUDA and Needleman-Wunsch). SARUMAN uses a qgram index based filter algorithm followed by a modified Needleman-Wunsch alignment. To speed up he normally time-consuming alignment step all alignments are processed on a NVIDIA graphics card to exploit the massive parallel architecture of new graphics processing units (GPUs).
Source: University of Bielefeld

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SeqMap

SeqMap is a tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides.
Source: SeqMap

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SHRiMP2

SHRiMP2 is a software package for mapping reads from a donor genome against a target (reference) genome. SHRiMP2 was primarily developed to work with short reads produced by Next Generation Sequencing (NGS) machines.
Source: University of Toronto

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Slider II

Slider II is an application for the Illumina Sequence Analyzer output that uses the probability files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences.
Source: BC Cancer Agency

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SNAP

SNAP is a new sequence aligner that is 3-20x faster and just as accurate as existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools (in some cases) and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.
Source: UC Berkeley Amp Lab

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SOAPaligner/soap2

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer.
Source: BGI

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SOAP3

SOAP3 is a GPU-based software for aligning short reads with a reference sequence.It can find all alignments with k mismatches, where k is chosen from 0 to 3 (see Section 3.2 for other options including finding only the best alignments and trimming the reads). When compared with its previous version SOAP2, SOAP3 can be up to tens of times faster. For example, when aligning length-100 reads with the human genome, SOAP3 is the first software that can find all 3-mismatch alignments in tens of seconds per one million reads.
Source: BGI

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SOCS

Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences.

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SpliceMap

SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths.
Source: Stanford University

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SSAHA2

SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.
SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.
Source: Wellcome Trust Sanger Institute

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Stampy

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions.
Source: Wellcome Trust Centre for Human Genetics

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STAR

STAR is an ultrafast universal RNA-seq aligner

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V-Profiler

V-Profiler takes a read alignment and a list of accepted variants at each location in the alignment (such as would be generated by V-Phaser) and analyzes the intra-host diversity of a genome.
Source: Broadinstitute

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ZOOM

Using ZOOM, zillions of short reads are mapped back to reference genomes, including post-analysis at unparalleled in speed, at full sensitivity.1 Throughout the next few pages, ZOOM's features, capabilities, even benchmarking will be presented, to provide researchers with as much information about the software as possible.
Source: Bioinformatics Solutions

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Genetic Linkage Mapping Software

HighMap

HighMap software is suitable for genetic map development by Biomarker Technologies Corporation. This software utilized maximum likelihood and smooth algorithm, and could deal with ten thousand markers that make map distance more stably. We now provide a network trial version for everyone who need to use it.
Source: Biomarker Technologies

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JoinMap

JoinMap ® Software for the calculation of genetic linkage maps in experimental populations of diploid species JoinMap provides high quality tools that allow detailed study of the experimental data and the generation of publication-ready map charts. The intuitive MS-Windows ® user interface of JoinMap invites to a better exploration of the data. For instance, you can perform several diagnostical tests, both before and after the actual map calculation, and you can remove potentially erroneous loci and individuals from the map calculations by a simple mouse-click.
Source:Kyazma

Lep-MAP2

Lep-MAP2 (LM2) is a novel linkage map construction suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them.
Source: Sourceforge

OneMap

OneMap is an environment for constructing linkage maps in several experimental crosses, including outcrossing (full-sib families derived from two non-homozygous parents), RILs, F2 and backcrosses.
Source: My Biosoftware

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R/qtl

R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses. It is implemented as an add-on package for the freely available and widely used statistical language/software R (see the R project homepage). The development of this software as an add-on to R allows us to take advantage of the basic mathematical and statistical functions, and powerful graphics capabilities, that are provided with R.
Source: RQTL

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