How can I analyse NGS data of microbiome (For beginner)?
I am beginner in the field of Bioinformatics and started analysing NGS data of microbiome. I would like to know what is the best software available to start analzsing sequencing files from MiSeq. I have started using Qiime but I do not know much of UNix command. Is there any book where it is described how to go about it from quality control, attaching barcode, pair end overlapping sequence, and then generation OTU tables and further analysis.
Even before deciding if you want to start coding, you might want to take a look at the Galaxy platform: https://usegalaxy.org/
It is a public online platform with a large number of bioinformatics tools, such as the NGS tools you might want to use. No coding knowledge is required, and there are information pages on all the tools within the platform. The computing is done on a queue bassis on their cluster, therefore also removing the need for high performing computer.
There are also available tutorials on Galaxy. It is a great starting point for biologists.
Thank you Dr. Werner for sending me the information. I have started working from that site but was finding difficulty to follow. I will check again updated version of tutorial. I guess I am a beginner and not used Unix commands so each and every step takes time to execute. I will get use to it soon suggested by everyone here. Thank you to all.
I did publish few 'systematic review and meta-analysis' papers in the recent-past in peer-reviewed international journals, however I have not registered those protocols in any database/registry before conduct OR publication.
In this regard, I want to know whether ''It is MANDATORY to register the protocol before conducting any Systematic reviews and meta-analysis?
I would request the experts in the domain to through some light on this.
The knowledge regarding microaerophilic and anaerobic Specific Spoilage Organisms (SSOs) is crucial for an appropriate evaluation of vacuum-packed ham. The objective of this study was to characterize the SSO community in vacuum-packed ham by culture-dependent technique and MiSeq next generation sequencing (NGS) platform. The relation b...
Premise of the study: Microsatellite primers were designed for Calochortus gunnisonii (Liliaceae), a montane lily species of the central and southern Rocky Mountains, using next-generation DNA sequencing. The markers will be used to investigate population structure, genetic diversity, and demographic history.
Methods and Results: Thirteen polymorph...