pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. ...
PGAP: pan-genomes analysis pipeline 来自 掌桥科研 喜欢 0 阅读量: 253 作者: Jun Yu 摘要: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. ...
PGAP: pan-genomes analysis pipeline. Bioinformatics. 2012; 28(3):416–8. https://doi.org/10.1093/bioinformatics/btr655. CAS PubMed Google Scholar Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. A low-polynomial algorithm for assembling clusters of ...
PGAP: pan-genomes analysis pipeline. Bioinformatics. 2012;28(3):416–8. https://doi.org/10.1093/bioinformatics/btr655. Article CAS PubMed Google Scholar Fouts DE, Brinkac L, Beck E, Inman J, Sutton G. PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-...
Create and activate a conda environment to run the bootstrapping script and the pipeline (named microGWAS, can be skipped if it's already present): conda env create -f environment.yml conda activate microGWAS 3. Prepare your phenotype file Save your phenotype table as a tab-separated file...
The remaining unmaskedB. napusgenome was annotated using a comprehensive strategy combining evidence-based and ab initio gene prediction. Using PASA and the EVM pipeline23, we incorporated protein sequences from six related species and the transcripts assembled from the RNA-seq data of each accession...
The core pipeline, TraFiC-mem (Supplementary Fig. 3)—which was used to explore somatic retrotransposition in PCAWG—was validated by single-molecule whole-genome sequencing data analysis of one cancer cell line with high retrotransposition rate and its matched normal sample, confirming the somatic ...
a universally present prophage will be classified as core and will be missed by this pipeline. Detection of IS may also be influenced by parameters used to construct pangenome. For example, Panaroo in--clean-mode strictwill tend to remove IS annotations at the end of contigs and may result...
in which we are interested in the driver mutations in a specific patient, these issues become substantially more important. Careful and critical appraisal of the whole pipeline—including sample acquisition, genome sequencing, mapping, variant calling and driver annotation, as done here—should be requ...
High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported. Here, we perform the pan-3D genome analysis using Hi-C sequencing data from