• Something wrong with this record ?

A combined de novo assembly approach increases the quality of prokaryotic draft genomes

U. Çabuk, ES. Ünlü

. 2022 ; 67 (5) : 801-810. [pub] 20220606

Language English Country United States

Document type Journal Article

Persistent link   https://www.medvik.cz/link/bmc22022920

Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.

References provided by Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc22022920
003      
CZ-PrNML
005      
20240416152628.0
007      
ta
008      
221007s2022 xxu f 000 0|eng||
009      
AR
024    7_
$a 10.1007/s12223-022-00980-7 $2 doi
035    __
$a (PubMed)35668290
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxu
100    1_
$a Çabuk, Uğur $u Faculty of Arts and Science, Department of Biology, Bolu Abant İzzet Baysal University, Bolu, Turkey $u Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany $u Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany $1 http://orcid.org/0000000244433065
245    12
$a A combined de novo assembly approach increases the quality of prokaryotic draft genomes / $c U. Çabuk, ES. Ünlü
520    9_
$a Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.
650    12
$a vysoce účinné nukleotidové sekvenování $x metody $7 D059014
650    _2
$a sekvenční analýza DNA $x metody $7 D017422
655    _2
$a časopisecké články $7 D016428
700    1_
$a Ünlü, Ercan Selçuk $u Faculty of Arts and Science, Department of Chemistry, Bolu Abant İzzet Baysal University, Bolu, Turkey. esunlu06@gmail.com $1 http://orcid.org/0000000300971125
773    0_
$w MED00011005 $t Folia microbiologica $x 1874-9356 $g Roč. 67, č. 5 (2022), s. 801-810
856    41
$u https://pubmed.ncbi.nlm.nih.gov/35668290 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y - $z 0
990    __
$a 20221007 $b ABA008
991    __
$a 20240416152625 $b ABA008
999    __
$a ok $b bmc $g 1845893 $s 1174206
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2022 $b 67 $c 5 $d 801-810 $e 20220606 $i 1874-9356 $m Folia microbiologica $n Folia microbiol. (Prague) $x MED00011005
LZP    __
$a Pubmed-20221007

Find record

Citation metrics

Archiving options