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https://github.com/franciscozorrilla/metaGEM A Snakemake-based workflow to generate high quality metagenome assembled genomes from short read paired-end data, reconstruct genome scale metabolic models, and perform community metabolic interaction simulations on high performance computing clusters.[……] […] https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-Tutorial-(Humann2) […] http://www.360doc.com/content/20/0823/10/71250389_931761136.shtml https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-standard-operating-procedure-v2 Note that this workflow is continually being updated. If you want to use the below commands be sure to keep track of them locally[……] […] BackgroundNext generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical meth[……] […] Utilities / Create consensus sequence from a BAM fileDescription Given an indexed BAM file and corresponding reference genome (in fasta format), this tool constructs a consensus sequence based on the alignment. Parameters None DetailsThis tool uses SAMtools, bcftools and vcfutils.pl script t[……] […] multiqc ranger ployly https://github.com/MultiQC https://github.com/ranger/ranger https://zhuanlan.zhihu.com/p/34369349 […] In statistics, data binning is a way to categorize a number of continuous values into a smaller number of buckets (bins). Each bucket defines an numerical interval. For example, if there is a variable about house-based education levels which are measured by continuous values ranged between 0 and 19,[……] […] https://guangchuangyu.github.io/2014/04/chipseeker-for-chip-peak-annotation/ ChIPpeakAnno WAS the only R package for ChIP peak annotation. I used it for annotating peak in my recent study. I found it does not consider the strand information of genes. I reported the bug to the authors, but they[……] […] In this tutorial, we’re going to take a set of Illumina reads from an inbred Drosophila melanogaster line, and map them back to the reference genome. (After these steps, we could do things like generate a list of SNPs at which this line differs from the reference strain, or generate a genome sequenc[……] […] [Originally posted by Kat on her BacPathGenomics blog, April 2013] This is a shameless plug for an article and accompanying tutorial I’ve just published together with David Edwards, my excellent MSc Bioinformatics student from the University of Melbourne. It’s currently available as a PDF pre-pub[……] […] |
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