What are good means for performing quality control (QC) or NGS reads?
I'm aware of:
- NGS Screen
- Kraken (e.g., for screening against contaminants)
What are other popular means for such QC?
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MultiQC can merge all your different reports into a single one. Which could be useful once you manage to know which QC tools to use.
There are then lots of QC tools specific to different types of data, most of which run after alignment. For example RSeQC (RNA data), Qualimap and many many others. Without specifying what kind of data you have this is a bit difficult to make recommendations for though.
The quality control of ngs reads is heavily dependent on type of the project.
For genome assembly projects based on short reads, beside already covered checking quality of sequencing, you would like to look at the kmer spectra to find out, if your reads are going to make sense when they will be translated to De Brujin graph. You will get also a clues about genome coverage, genome size, repetitive content and small clue about heterozygocity. A lot of useful info about interpretation you can find in the README of GenomeScope.
A list tools I used:
Using these tools can save you a lot of frustration if you accidentally sequence a contaminated sample or if your colleagues / a sequencing company have sent you a wrong file!
The kind of QC you do routinely depends on what your lab's focus is. We do a lot of low-quality, multiplexed DNA and RNA. If you routinely do fresh frozen whole genomes, your QC will be different.
Weighing in from the resequencing side of things (i.e. sequencing an organism that has a good reference), there are several things we are testing with quality control:
You may use a combination of tools:
If you are looking for NGS QC for your fastq, bam, bed and vcf files I would suggest a commercial tool called omnomicsQ.
It automates coverage analysis and sample pass, warn fail according according to your defined SOPs. Unlike fastqc it also comes with a database so that you can compare protocols, samples, and your performance to peer organisations. It also charts performance over time, exceptions,and correlations between metrics