A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.
Takes a paired-end Illumina fastq file generated from an RNA-seq library, and that has been error corrected with rCorrector, see Song and Florea 2015, Gigascience,and removes reads with errors but that are unfixable, and strips 'cor' flags from reads that were corrected.
Parses the fastqc output files to retrieve over-represented sequences, and uses these to remove read pairs where either read has a sequence match to an over-represented sequence.