Metagenomics standard operating procedure v2

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.

Last updated: 9 Oct 2018 (see revisions above for earlier minor versions and Metagenomics SOPs on the SOP for earlier major versions)

Important points to keep in mind:

The […]

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples

Background

Next 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 methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory […]

Utilities / Create consensus sequence from a BAM file

Utilities / Create consensus sequence from a BAM file Description

Given an indexed BAM file and corresponding reference genome (in fasta format), this tool constructs a consensus sequence based on the alignment.

Parameters

None

Details

This tool uses SAMtools, bcftools and vcfutils.pl script to create a consensus sequence for the given alignment file. The actual […]

Good software

multiqc ranger ployly

https://github.com/MultiQC

https://github.com/ranger/ranger

https://zhuanlan.zhihu.com/p/34369349

Data Binning and Plotting

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, data binning will place each value […]

ChIPseeker for ChIP peak annotation (转贴)

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 are reluctant to change.

So I decided to develop my own package, ChIPseeker, and […]

Mapping reads with bwa and bowtie

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 sequence for this […]

BACTERIAL GENOMICS TUTORIAL (repost)

[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 from BMC Microbial Informatics and Experimentation, but the web version […]

POPULATION GENOMICS OF KLEBSIELLA (Repost)

https://holtlab.net/2015/06/23/population-genomics-of-klebsiella/

Well, after almost 6 years, our Klebsiella pneumoniae genomics paper is finally out!

It’s a beast of a thing and there are still a million and one questions to address just from this one data set. For those interested in looking at the data for themselves, the raw reads are available under accessionERP000165, the […]

TOOLS FOR BACTERIAL COMPARATIVE GENOMICS

Yesterday I spoke at a workshop for JAMS TOAST (Sydney’s Joint Academic Microbiology Seminars – bioinformatics workshop)… I was asked to cover tools for comparative genomics, so I put together a list of the tried and tested programs that I find most useful for this kind of analysis. So here is the list.