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Index construction software tools | High-throughput sequencing analysis

FM-index plays an important role in DNA sequence alignment, de novo assembly (Simpson and Durbin, 2012) and compression (Cox et al., 2012). Fast and lightweight construction of FM-index for a large dataset is the key to these applications. Source…
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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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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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sBWT
Desktop

sBWT

A highly hardware-acceleration friendly k-ordered FM-index for exact string…

A highly hardware-acceleration friendly k-ordered FM-index for exact string matching, overlap graph construction for de novo assembly, and more. sBWT is a Burrows–Wheeler transform (BWT) based fast…

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FMtree
Desktop

FMtree

Accelerates the locating operation of FM-indexes for genomic data. FMtree is a…

Accelerates the locating operation of FM-indexes for genomic data. FMtree is a locating algorithm that permits to build a conceptual multiway tree. By utilizing this multiway tree, FMtree is able to…

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GIGGLE
Desktop

GIGGLE

Allows users to conduct large-scale comparisons of their results with thousands…

Allows users to conduct large-scale comparisons of their results with thousands of reference datasets and genome annotations in seconds. GIGGLE permits to identify novel and unexpected relationships…

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Goleft
Desktop

Goleft

Enables coverage profiling at low computational cost, provides an interactive…

Enables coverage profiling at low computational cost, provides an interactive output that facilitates the detection of coverage anomalies (deletions, duplications, sex chromosome anomalies). Goleft…

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Tabix
Desktop

Tabix

Indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL,…

Indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves features overlapping specified regions. Tabix features include few seek…

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ropeBWT
Desktop

ropeBWT

A tool for constructing the FM-index for a collection of DNA sequences. ropeBWT…

A tool for constructing the FM-index for a collection of DNA sequences. ropeBWT works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting…

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kFM-index
Desktop

kFM-index

Provides a compact storage of de Bruijn subgraphs representing the k-subwords…

Provides a compact storage of de Bruijn subgraphs representing the k-subwords of a set of strings.

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dbifasta
Desktop

dbifasta

Indexes a fasta file database. dbifasta needs a flat file database of one or…

Indexes a fasta file database. dbifasta needs a flat file database of one or more files, and builds EMBL CD-ROM format index files. The resulting index-file format is used by the software on the EMBL…

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dbxtax
Desktop

dbxtax

Indexes NCBI taxonomy using b+tree indices. dbxtax creates one summary file for…

Indexes NCBI taxonomy using b+tree indices. dbxtax creates one summary file for the database and two files for each field indexed.

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