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Bowtie
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Aligns short read geared toward mammalian re-sequencing. Bowtie is based on a Burrows-Wheeler index based on the full-text minute-space (FM) index. It follows two steps: an initial, ungapped seed-finding stage that derives advantage from the speed and memory efficiency of the full-text minute index and a gapped extension stage that employs dynamic programming and benefits from the efficiency of single-instruction multiple-data (SIMD) parallel processing available on modern processors.
CORA / COmpressive Readmapping Accelerator
Achieves substantial runtime improvement through the use of compressive representation of the reads and a comprehensive homology map of the reference genome, when plugged into existing mapping tools. CORA’s compressive framework achieves speed gains inversely related to the sequencing error rate, the acceleration it provides will substantially improve as sequencers generate higher-quality reads. Furthermore, CORA constructs a reference homology table data structure, which also offers general utility beyond read mapping by providing fast access to all pairs of homologous loci in the reference genome.
BWA / Burrows-Wheeler Aligner
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Performs short read alignments. BWA can be used for : gapped aligning for single-end reads, paired-end mapping and mapping quality. It is composed of three algorithms: (i) BWA-backtrack, for Illumina sequence reads up to 100bp; (ii) BWA-SW for local alignments including long-read support and split alignment and (iii) BWA-MEM, that consists of an aligner for sequence reads able to work for both 70bp reads and long sequences up to a few megabases.
MIA / Mapping Iterative Assembler
The basic idea of this program is to align DNA sequencing fragments (shotgun or targeted resequencing) to a reference, then call a consensus. Then the consensus is used as new reference and the process is repeated until convergence. Since it was originally designed to be used on ancient DNA, it supports a position specific substitution matrix, which improves both alignment and consensus calling on chemically damaged aDNA. MIA has been used to assemble a number of Neandertal and early modern human mitochondria.
MAQGene
Allows read alignment as well as single nucleotide polymorphism (SNP) detection and annotation. MAQGene launches the MAQ software and assembles a customized summary of the location and specific features of sequence variants of the mutant genome compared to a wild-type reference genome. The software also provides the option to compare any input whole genome sequencing (WGS) reads to any wild-type available reference genome with general-feature format (GFF) coding exon annotations files.
MECAT / Mapping Error Correction and de novo Assembly Tool
Aligns sequences with or without local alignment. MECAT is a program based on a pseudolinear alignment scoring algorithm that exploits distance difference factors (DDFs). The software is composed of four modules: (i) a single molecule real time (SRMT) reads pairwise mapper, (ii) an SMRT reads reference mapper; (iii) a noise corrector and (iv) a pipeline for hierarchical assembly which is an extension version of the CANU pipeline.
BLAT / BLAST-Like Alignment Tool
Finds genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is a very fast sequence alignment tool similar to BLAST typically used for searching similar sequences within the same or closely related species. It was developed to align millions of expressed sequence tags and mouse whole-genome random reads to the human genome at a higher speed. BLAT is commonly used to look up the location of a sequence in the genome or determine the exon structure of an mRNA, but expert users can run large batch jobs and make internal parameter sensitivity changes by installing command line it on Linux server.
CUSHAW
Consists of algorithm for parallel, sensitive, and accurate next-generation sequencing (NGS) read alignment to large genomes such as human genome. CUSHAW is a software suite and is composed of three individual software tools, namely CUSHAW, CUSHAW2, and CUSHAW3. This suite employs inexact k-mer seeds (for CUSHAW); adopts MEM seeds (for CUSHAW2); and introduces hybrid seeds incorporating three different seed types (for CUSHAW3), i.e., MEM seeds, exact-match kmer seeds, and variable-length seeds derived from local alignments.
dDocent
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Offers a platform for population-level analyses. dDocent is an open-source software dedicated to individually barcoded restriction-site associated DNA sequencing (RADseq) data processing. The application employs data reduction techniques and interact with other programs to propose features such as de novo assembly of RAD loci, single nucleotides polymorphisms (SNPs) and indel calling as well as quality trimming or baseline data filtering.
LAST
Enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition. LAST can handle big sequence data, e.g: compare two vertebrate genomes and align billions of DNA reads to a genome. It indicates the reliability of each aligned column and uses sequence quality data properly. LAST compares DNA to proteins with frameshifts, compares position-specific scoring matrices (PSSMs) to sequences, calculates the likelihood of chance similarities between random sequences and does split and spliced alignment. Furthermore, it trains alignment parameters for unusual kinds of sequence (e.g. nanopore). LAST is available as a web application or can be download for local use.
MAQ / Mapping and Assembly with Quality
Builds mapping assemblies from short reads generated by the next-generation sequencing machines. Maq is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data. 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. At the assembling stage, maq calls the consensus based on a statistical model.
RSF / RNA Structure Framework
Deals with RNA structure probing and post-transcriptional modifications mapping high-throughput data. RNA Framework is a modular toolkit. Its main features are (i) automatic reference transcriptome creation, (ii) automatic reads preprocessing (adapter clipping and trimming) and mapping, (iii) scoring and data normalization and (iv) accurate RNA folding prediction by incorporating structural probing data. It can perform not only RNA Structure analysis, but also analysis of RNA post-transcriptional modifications mapping experiments (such as m1A-seq, m6A-seq, 2OMe-seq, and Pseudo-seq).
Stacks
Builds genetic maps and conducts population genomics and phylogeography. Stacks is a software system developed to work with restriction enzyme-based data, such as RAD-seq. The software produces core population genomic summary statistics and single nucleotide polymorphism (SNP)-by-SNP statistical tests. It aims to be a key resource to empower researchers to efficiently perform ecological and evolutionary genomic studies in model organisms and particularly in organisms with minimal or no genomic resources.
GraphMap
Analyses nanopore sequencing reads. GraphMap progressively refines candidate alignments to robustly handle potentially high-error rates and a fast graph traversal to align long reads with speed and high precision (>95%). Its alignments enabled single-nucleotide variant calling on the human genome with increased sensitivity (15%) over the next best mapper, precise detection of structural variants from length 100 bp to 4 kbp, and species and strain-specific identification of pathogens using MinION reads.
Qtip
Operates alongside and in cooperation with an aligner like Bowtie 2. Qtip runs alongside a read aligner and builds an input model, simulates tandem reads, aligns those using the same aligner and parameters, then uses the trained model to predict mapping qualities. It works with any aligner that outputs feature data in a special SAM field. This framework is also applicable to specialized alignment settings, such as spliced RNA-seq alignment. In that case, a nuanced notion of correctness is needed.
BBMap
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Uses as a splice-aware aligner for short and long reads. BBMap is shown to be a fast and accurate aligner, capable of correctly handling an overall wider variety of references, reads, and mutations than others. It has particularly outstanding performance with deletions, especially long ones, that other aligners cannot handle at all. It can output many different statistics files, such as an empirical read quality histogram, insert-size distribution, and genome coverage, with or without generating a sam file.
RAMICS / Rapid Amplicon Mapping in Codon Space
A hidden Markov model reference mapper, designed to align coding and non-coding DNA to a reference sequence. By default, RAMICS assumes DNA is coding and Sanger-sequenced. Options allow the user to specify the sequencing platform used for more accurate alignment. RAMICS can also be set to training mode, where it will iteratively refine the profile hidden Markov model associated with the reference sequence to the profile of the query sequences aligned to it.
COSINE / ClOse-range Spectral ImagiNg of lEaves
Aligns long sequences with high variations or errors including insertions and deletions to the target. COSINE has a predictable computational resource usage for mapping reads from E. coli genome, S. coelicolor genome with high GC conect or complex human genome. This tool is able to maintain a high alignment accuracy in a wide range of error rates and genome sizes with minimal tuning. It can be a software aligner or can retrieve skipped reads.
CLC bio / CLC Genomics Workbench
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Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
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