Instructionįind more organelle genome assembly instruction at GetOrganelle/wiki. You are going to get a similar running log as here and the same result as here.įind more real data examples at GetOrganelle/wiki/Examples, GetOrganelleGallery and GetOrganelleComparison. Get_organelle_from_reads.py -1 Arabidopsis_simulated.1.fq.gz -2 Arabidopsis_simulated.2.fq.gz -t 1 -o Arabidopsis_astome -F embplant_pt -R 10 The easiest way to install GetOrganelle and its dependencies is using conda: Windows Subsystem Linux is currently not supported, we are working on this. GetOrganelle is currently maintained under Python 3.7.0, but designed to be compatible with versions higher than 3.5.1 and 2.7.11. Bandage: interactive visualization of de novo genome assemblies. BMC Bioinformatics 10: 421.īandage: Wick, R. Fast gapped-read alignment with Bowtie 2. Journal of Computational Biology 19: 455-477.īowtie2: Langmead, B. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Please also cite the dependencies if used: ![]() GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Please denote the version of GetOrganelle as well as the dependencies in your manuscript for reproducible science.Ĭitation: Jian-Jun Jin*, Wen-Bin Yu*, Jun-Bo Yang, Yu Song, Claude W.
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