Enumerated Automata Implementation of String Dictionaries

Bakarić, Robert; Korenčić, Damir; Ristov, Strahil

doi:10.1007/978-3-030-23679-3_3

Cited by 1 publication

(2 citation statements)

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“…Alternatively, in order to produce a succinct FASTQ representation, it would be possible to use some other approach to compress of a set of strings, with different trade-offs in construction parameters. Some of the competing methods are listed in [11]. Still, we believe that LZ trie is the most useful compromise-especially so if the input strings are long, as in a FASTQ record.…”

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

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

confidence: 99%

“…This is in accordance with our previous findings. In [11] we have compared the response times of automata and BWT-based structures and automata were several times faster, albeit in a different retrieval task.…”

Section: Datasetmentioning

confidence: 99%