'High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing'
#plantsci #genomics #bioinformatics
https://doi.org/10.1101/2020.01.31.928630 …pic.twitter.com/7mEAiWSTHs
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Corresponding #Python scripts are available @github:
https://github.com/bpucker/yam
Sequence read data sets are submitted to @enasequence. Annotation and associated files are available here:
https://bit.ly/37UorGK
#opensource #datasharing #opensciencehttps://bit.ly/2UfWLZb
Highly heterozygous genome is partially phase-separated in the assembly with #ONT long reads. @illumina short reads were mapped to classify predicted genes as merged/phased based on coverage and sequence variants (#GATK)
https://bit.ly/2UfWLZb pic.twitter.com/3oDZrA5bHz
1) CTAB-based #DNA extraction
2) short fragment removal via SRE @circulomics
3) @nanopore sequencing
4) Canu assembly
5) Racon polishing with #ONT long reads
6) Medaka polishing with #ONT long reads
7) Pilon polishing with @illumina short reads
https://bit.ly/2UfWLZb pic.twitter.com/khGzNQEOB3
Submitted about 1TB of sequence read data for this yam genome project to @enasequence (underlying fast5 files are included). It might take a couple of days until all files are available.
#opendata #openscience #reusehttps://bit.ly/2UfWLZb
Amazing knowledge about Arabidopsis thaliana genes is often harnessed for the functional annotation of predicted genes. Many thanks to the great community for providing this valuable resource! @tair_news
#basicresearch #plantscihttps://bit.ly/2UfWLZb
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