<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44591?offset=70 https://bioinformaticsonline.com/bookmarks/view/43353/judi-just-do-it Mon, 06 Sep 2021 02:44:35 -0500 https://bioinformaticsonline.com/bookmarks/view/43353/judi-just-do-it <![CDATA[JUDI: Just Do It]]> judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings.

https://github.com/ncbi/JUDI

Address of the bookmark: https://github.com/ncbi/JUDI

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44375/phyloherb-a-high%E2%80%90throughput-phylogenomic-pipeline-for-processing-genome-skimming-data Wed, 06 Sep 2023 00:14:28 -0500 https://bioinformaticsonline.com/bookmarks/view/44375/phyloherb-a-high%E2%80%90throughput-phylogenomic-pipeline-for-processing-genome-skimming-data <![CDATA[PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data]]> Phylogenomic Analysis Pipeline for Herbarium Specimens

What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a high throughput program dealing with lower quality data. Examples include low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data, retrieving low-copy nuclear genes from medium coverage (5x nucDNA) genome skimming.

License: GNU General Public License

Citation:

  • Cai, Liming, Hongrui Zhang, and Charles C. Davis. 2022. PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome‐skimming data. Applications in Plant Sciences 10(3): 1–9. https://doi.org/10.1002/aps3.11475

Address of the bookmark: https://github.com/lmcai/PhyloHerb/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44597/imagine-in-silico-metagenomics-pipeline Sat, 06 Jul 2024 04:32:18 -0500 https://bioinformaticsonline.com/bookmarks/view/44597/imagine-in-silico-metagenomics-pipeline <![CDATA[iMAGine - in silico MetAGenomics pipeline]]> iMAGine is a metagenomic workflow which includes filtering, assembling, and binning.

This workflow includes the following tools which are needed to be installed in the system.

  1. fastp
  2. spades assembler
  3. QUAST
  4. bwa
  5. samtools
  6. metabat2
  7. CheckM

Address of the bookmark: https://github.com/avishekdutta14/iMAGine

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