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Fragment recruitment (metagenomic analysis)

Fragment recruitment, a process of aligning sequencing reads to reference genomes, is a crucial step in metagenomic data analysis to analyze the phylogenetic composition, genes and functions of the samples. This procedure was introduced in the…
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Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its…

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BWA
Desktop

BWA Burrows-Wheeler Aligner

Maps low-divergent sequences against a large reference genome, such as the…

Maps low-divergent sequences against a large reference genome, such as the human genome. BWA consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for…

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BLAT
Desktop
Web

BLAT BLAST-Like Alignment Tool

Finds genomic sequences that match a protein or DNA sequence submitted by the…

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…

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SSAHA
Desktop

SSAHA Sequence Search and Alignment by Hashing Algorithm

A pairwise sequence alignment program designed for the efficient mapping of…

A pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA reads of most sequencing platforms (ABI-Sanger, Roche 454,…

BLASTN
Web

BLASTN Standard Nucleotide BLAST

Programs search nucleotide databases using a nucleotide query. BLASTN key…

Programs search nucleotide databases using a nucleotide query. BLASTN key features are searching with short sequencing and cross-species comparison.

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MegaBLAST
Desktop

MegaBLAST

Allows nucleotide sequence alignment search. MegaBLAST finds seeds by searching…

Allows nucleotide sequence alignment search. MegaBLAST finds seeds by searching an index structure of k-mers derived from preprocessing the database. MegaBLAST module is included in the blastn…

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LAST-TRAIN
Desktop
Web

LAST-TRAIN

Improves sequence alignment accuracy by inferring substitution and gap scores…

Improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. LAST-TRAIN uses a standard…

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FR-HIT
Desktop

FR-HIT

An efficient fragment recruitment program for next generation sequences against…

An efficient fragment recruitment program for next generation sequences against microbial reference genomes.

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FACS
Desktop

FACS Fast and Accurate Classification of Sequences

Allows to assembly filters from genome sequences and apply a filter to a file…

Allows to assembly filters from genome sequences and apply a filter to a file of sequence reads. FACS classifies sequence reads as belonging to one of many reference sequences or being ‘novel’.…

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MetaSpark
Desktop

MetaSpark

Recruits metagenomic reads to reference genomes. For each task, MetaSpark uses…

Recruits metagenomic reads to reference genomes. For each task, MetaSpark uses a join operation to connect with the KmerStr of RefindexRDD. MetaSpark scans the k-mer RefindexRDD to collect the k-mers…

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BLASTPLOT
Desktop

BLASTPLOT

A PERL module to quickly plot the BLAST results from short sequences (primers,…

A PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets.

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