Fast construction of space‐optimized recursive automaton

Ristov, Strahil; Korenčić, Damir

doi:10.1002/spe.2261

Cited by 4 publications

(3 citation statements)

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“…The core of our implementation of a succinct FASTQ format is the LZ trie, the stateof-the-art method for automata compression [9] that is incorporated into our SFQ (https: //github.com/lisp-rbi/sfq, accessed on 10 May 2022) software for the construction and querying of sFASTQ. The drawbacks of employing automata are considerable memory consumption and the time needed for construction.…”

Section: Overviewmentioning

confidence: 99%

“…The state-of-the-art in deterministic automata compression, regarding the compression factor and the construction speed, is the LZ trie algorithm. The details on LZ trie can be found in [9]; here we give a brief description. A trie is a digital tree that represents a set of strings by storing the shared prefixes only once.…”

Section: Sfastq Data Structures Implementation Details 221 Lz Trie Da...mentioning

confidence: 99%

“…This feature is implemented by persisting the LZ trie data structure in a format that mirrors its representation in RAM. The LZ trie structure is represented as an array that holds the nodes of the trie [9]. This array is encapsulated as an abstract TNodeArray type, which enabled us to transparently switch to disk storage by implementing the on-disk array with the same interface.…”

Section: On Lz Trie Implementationmentioning

confidence: 99%

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SFQ: Constructing and Querying a Succinct Representation of FASTQ Files

et al. 2022

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A large and ever increasing quantity of high throughput sequencing (HTS) data is stored in FASTQ files. Various methods for data compression are used to mitigate the storage and transmission costs, from the still prevalent general purpose Gzip to state-of-the-art specialized methods. However, all of the existing methods for FASTQ file compression require the decompression stage before the HTS data can be used. This is particularly costly with the random access to specific records in FASTQ files. We propose the sFASTQ format, a succinct representation of FASTQ files that can be used without decompression (i.e., the records can be retrieved and listed online), and that supports random access to individual records. The sFASTQ format can be searched on the disk, which eliminates the need for any additional memory resources. The searchable sFASTQ archive is of comparable size to the corresponding Gzip file. sFASTQ format outputs (interleaved) FASTQ records to the STDOUT stream. We provide SFQ, a software for the construction and usage of the sFASTQ format that supports variable length reads, pairing of records, and both lossless and lossy compression of quality scores.

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Section: Overviewmentioning

confidence: 99%

Section: Sfastq Data Structures Implementation Details 221 Lz Trie Da...mentioning

confidence: 99%

Section: On Lz Trie Implementationmentioning

confidence: 99%

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