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BLAST / Basic Local Alignment Search Tool
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Allows to align query sequences against those present in a selected target database. BLAST is a suite of programs, provided by NCBI, which can be used to quickly search a sequence database for matches to a query sequence. The software provides an access point for these tools to perform sequence alignment on the web. The set of BLAST command-line applications is organized in a way that groups together similar types of searches in one application.
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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.
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.
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.
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.
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
Employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assembling large genomes. It achieves superior computing efficiency to current assembly pipelines. In particular, MECAT takes only about 7600 CPU core hours to assemble a high quality human CHM1 genome using 54x SMRT data47 (CHM1) on a single 32-threads computing node with 2.0 GHz CPU, which is 34 times faster than the current PBcR-MHAP pipeline. It makes it possible to de novo assemble large genome using Single Molecule Real Time (SMRT) reads with the similar computational cost as that the assembling of Next Generation Sequencing (NGS) reads needs.
mrsFAST / Micro-read substitution-only Fast Alignment Search Tool
A fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of high throughput sequencing reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNPaware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode.
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.
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.
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Designed to process individually barcoded Restriction-site associated DNA sequencing (RADseq) data (with double cut sites) into informative single nucleotide polymorphisms (SNPs)/Indels for population-level analyses. dDocent uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage.
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.
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.
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.
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.
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.
A read mapper that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome. The software outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads. NextGenMap handles automatically any read data independent of read length and sequencing technology. It may be used to map reads from nonstandard organism to a phylogenetically close reference genome or to apply it to metagenomics data.
SAMSA / Simple Analysis of Metatranscriptome Sequence Annotations
Analyzes and characterizes activity within a metatranscriptome. SAMSA has four phases: (1) the preprocessing phase trims and combines reads for input to the annotation phase; (2) the annotation phase provides an annotation for each read; (3) the aggregation phase aggregates organism and function information across all reads; and (4) the analysis phase provides visualizations and statistical analysis. It runs either in-house or in conjunction with Metagenome-RAST (MG-RAST) servers.
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