FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/),  which can evaluate multiple aspects of the raw sequencing data quality, such as per base quality, per base GC content and sequence length distribution. It provides the user a quick overview of whether the data has any problems, which isuseful for a rough assessment of the data quality.

Fastx-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/),  which is a collection of command line tools for short-reads FASTA/FASTQ files preprocessing, including read length trimming, identical reads collapsing, adapter removing, format converting, etc.

PRINSEQ, which provides more detailed options for some quality control functions. For example, for the duplication filtration, it can trim either exact duplicates or 5‘/3’ duplicates.  

文章：Quality control and preprocessing of metagenomic datasets （http://bioinformatics.oxfordjournals.org/content/early/2011/01/27/bioinformatics.btr026）

NGS QC Toolkit, which is another toolkit for NGS data quality control, comprised of tools for QC of sequencing data generated using Roche 454 and Illumina platforms.

文章：NGS QC Toolkit: A Toolkit for Quality Control of NextGeneration Sequencing Data （http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030619）

QC-Chain, a fast and holistic NGS data QC package, which can perform fast and de novo contamination screening on NGS genomic data.

文章：QC-Chain: Fast and Holistic QualityControl Method for Next-Generation Sequencing Data （http://www.ncbi.nlm.nih.gov/pubmed/23565205）

参考资料：Assessment of quality control approaches for metagenomic data analysis   2014  （https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223665/）