Quality control Tools

HTStream is a quality control and processing pipeline for High Throughput Sequencing data. The difference between HTStream and other tools is that HTStream uses a tab delimited fastq format that allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data and makes it fully interoperable with other standard Linux tools.

KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the host. However, sequencing data from such experiments will often contain a high ratio of host to bacterial reads. This tool aims to perform principled in silicoseparation of bacterial reads from these "contaminant" reads, be they from the host, from bacterial 16S sequences, or other user-defined sources.

LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc.

MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

NanoFilt is a streaming filtering tool for Oxford Nanopore sequencing data in FASTQ format, enabling filtering based on minimum read quality, length, and GC content, as well as trimming of nucleotides from read ends.

NanoLyse is a streaming tool for removing contaminant DNA reads (such as lambda phage control DNA) from Oxford Nanopore FASTQ files using the Minimap2 aligner, with minimal memory footprint for integration into sequencing pipelines.