Any FastQC alternative

Question

[eric.enns]

I am looking for a FastQC alternative, we run FastQC on our cluster which doesn't work so well with java. By that I mean java is incapable of listening to slurm resource limits and tries to allocate way more memory than it actually needs. Since we have a heterogenous cluster this means that we have to set FastQC to request more than 32GB of ram per execution, which just wastes resources.

[samuelandjw]

Why would java listen to slurm resource limits? Shouldn't you ask slurm to accommodate java by setting --mem instead?

Answer 1

[GenoMax]

@Matt Shirley's fastqp generates plots similar to FastQC.

fastp (LINK) can also generate these plots.

Answer 2

[spvensko]

I cannot speak to how well any of these work with SLURM but https://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools#Quality_control lists a few alternatives.

Another alternative not listed is fastx_quality_stats.sh (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_statistics_usage).

I've also used fastq-stats (part of the ea-utils suite: https://github.com/ExpressionAnalysis/ea-utils) quite a bit.

None of these options are, to the best of my knowledge, as full-fledged as FASTQC feature-wise, but they may play better with SLURM resource allocation.

Answer 3

[EagleEye]

You can also try this tool,

FaQCs (Perl)

https://github.com/LANL-Bioinformatics/FaQCs

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0366-2

Answer 4

[Carlos Caicedo]

Quack is also an alternative that according to their authors is faster than FASTQC and other tools

https://www.sciencedirect.com/science/article/pii/S0003269718300630