2023
DOI: 10.1111/2041-210x.14075
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MitoGeneExtractor: Efficient extraction of mitochondrial genes from next‐generation sequencing libraries

Abstract: Mitochondrial DNA (mtDNA) sequences are often found as byproducts in next‐generation sequencing (NGS) datasets that were originally created to capture genomic or transcriptomic information of an organism. These mtDNA sequences are often discarded, wasting this valuable sequencing information. We developed MitoGeneExtractor, an innovative tool which allows to extract mitochondrial protein coding genes (PCGs) of interest from NGS libraries through multiple sequence alignments of sequencing reads to amino acid re… Show more

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Cited by 3 publications
(2 citation statements)
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“…HMM-based tools are thus commonly used for sequence extraction. MitoGeneExtractor [10] and MitoFinder [11] are widely used for extracting mitochondrial COI, ITSx is used for extracting fungal ITS [12], Metaxa2 is used for extracting small and large subunit rRNA from bacteria, archaea, and fungi [13], and V-Xtractor is used for extracting various highly variable regions of the small subunit rRNA (16S/18S) sequence from bacteria, archaea, and fungi [14]. Among them, V-Xtractor can recognize and extract various hypervariable regions of the 18S rRNA gene.…”
Section: Introductionmentioning
confidence: 99%
“…HMM-based tools are thus commonly used for sequence extraction. MitoGeneExtractor [10] and MitoFinder [11] are widely used for extracting mitochondrial COI, ITSx is used for extracting fungal ITS [12], Metaxa2 is used for extracting small and large subunit rRNA from bacteria, archaea, and fungi [13], and V-Xtractor is used for extracting various highly variable regions of the small subunit rRNA (16S/18S) sequence from bacteria, archaea, and fungi [14]. Among them, V-Xtractor can recognize and extract various hypervariable regions of the 18S rRNA gene.…”
Section: Introductionmentioning
confidence: 99%
“…Notable exceptions include MitoZ (Meng et al, 2019) and NOVOWrap (Wu et al, 2021) for the assembly and annotation of mitochondrial genomes. MitoGeneExtractor can be used to extract mitochondrial protein coding genes from next generation sequencing datasets (Brasseur et al, 2023). In addition, plastaumatic (W. Chen et al, 2022) is available for chloroplast assembly and annotation and PhyloHerb (Cai et al, 2022) can be used for the assembly of chloroplast and nuclear ribosomal repeats without annotation.…”
Section: Introductionmentioning
confidence: 99%