Table 1 Information about the mitochondrial genome assemblers utilized in this study
From: A systematic comparison of human mitochondrial genome assembly tools
Tool | Source repository | Links for docker images available online | Reference genome dependency | Main approach | Programming language | License | Miscellaneous features | Multithreading support | Input data |
|---|---|---|---|---|---|---|---|---|---|
ARC | https://hub.docker.com/repository/docker/nirmal2310/arc_docker/ | Yes | Mapping to the reference genome followed by de novo assembly. | Python 2 | Apache License 2.0 | NA | Yes | Paired-End Illumina Fastq Files (Unzipped) | |
GetOrganelle | https://hub.docker.com/repository/docker/nirmal2310/getorganelle_docker/ | Yes | Mapping to the reference genome followed by de novo assembly. | Python 3 | GNU GPL v3.0 | NA | Yes | Paired-End/Single-End Illumina Fastq Files (Can be Gzipped) | |
IOGA | https://hub.docker.com/repository/docker/nirmal2310/ioga_docker/ | Yes | Mapping to the reference genome followed by de novo assembly. | Python 2 | GNU Affero GPL v3.0 | NA | Yes | Paired-End/Single-End Illumina Fastq Files (Can be Gzipped) | |
MEANGS | https://hub.docker.com/repository/docker/nirmal2310/meangs_docker/ | No | De novo Assembly | Python 3 | GNU GPL v3.0 | NA | Yes | Paired-End/Single-End Illumina Fastq Files (Can be Gzipped) | |
MITObim | https://hub.docker.com/repository/docker/nirmal2310/mitobim_docker/ | Yes | Mapping to the reference genome followed by de novo assembly. | Perl | MIT LICENSE | NA | No | Paired-End/Single-End Illumina Fastq Files (Paired-End should be Interleaved and Unzipped) | |
MitoFlex | https://hub.docker.com/repository/docker/nirmal2310/mitoflex_docker/ | No | De novo assembly | Python 3 | GNU GPL v3.0 | Genome annotation | No | Paired-End/Single-End Illumina Fastq Files (Can be Gzipped) | |
MitoZ | https://hub.docker.com/repository/docker/nirmal2310/mitoz_docker/ | No | De novo assembly | Python 3 | GNU GPL v3.0 | Genome annotation | Yes | Paired-End/Single-End Illumina Fastq Files (Can be Gzipped) | |
MToolBox | NA | Yes | Mapping to the reference genome followed by de novo assembly. | Python 2 | GNU GPL v3.0 | Haplogroup Prediction, Variant Calling | Yes | Paired-End/Single-End Illumina Fastq Files (Can be Gzipped) | |
NOVOPlasty | https://hub.docker.com/repository/docker/nirmal2310/novoplasty_docker/ | Yes | Seed and extend approach | Perl | NA | NA | No | Paired-End/Single-End Illumina Fastq Files (Can be Gzipped) | |
(Can be a single gene sequence) | |||||||||
ORG.Asm | https://hub.docker.com/repository/docker/nirmal2310/org-asm_docker/ | Yes | Seed and extent approach | Python 3 | CeCILL LICENSE | NA | No | Paired-End/Single-End Illumina Fastq Files (Can be Gzipped) | |
(Can be a single gene sequence) |