Once samples pass initial sequencing quality metrics generated by the sequencers, they are assessed by FASTQC that checks for per-base sequence quality, GC content, and N content, among others. If the data indeed looks sub-par, they will be immediately reprepped and resequenced. Data trimming is done if needed using any one of:
We also use tools such as phantompeakqualtools and HOMER to get highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.