Hi, this tool may save your time, it do filtering and QC with fastq data automatically

following introduction is out of date and the newer AfterQC is much more powerful, please check the github page for update

AfterQC

project on github: https://github.com/OpenGene/AfterQC
sample report: http://opengene.org/AfterQC/report.html

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair.
Currently it supports processing data from HiSeq 2000/2500/3000/4000, X10, X5, Nextseq 500/550, MiniSeq...

Features:

AfterQC does following tasks automatically:

• Filters reads with too low quality, too short length or too many N
• Filters reads with abnormal PolyA/PolyT/PolyC/PolyG sequences
• Does per-base quality control and plots the figures
• Trims reads at front and tail, according to QC results
• For pair-end sequencing data, AfterQC automatically corrects low quality wrong bases in overlapped area of read1/read2
• Detects and eliminates bubble artifact caused by sequencer due to fluid dynamics issues
• Single molecule barcode sequencing support: if all reads have a single molecule barcode (see duplex sequencing), AfterQC shifts the barcodes from the reads to the fastq query names
• Support both single-end sequencing and pair-end sequencing data

Dependency:

AfterQC uses editdistance module, run following before using AfterQC:

pip install editdistance

WARNING: If you haven't installed editdistance module, AfterQC will use a python implementation of editdistance, but it will be extremely slow.

Simple usage:

1, Prepare your fastq files in a folder
2, For single-end sequencing, the filenames in the folder should be *R1*
For pair-end sequencing, the filenames in the folder should be *R1* and *R2*

cd /path/to/fastq/folder
python path/to/AfterQC/after.py

Two folders will be automatically generated, a folder 'good' stores the good reads and a folder 'bad' stores the bad reads
AfterQC will print some statistical information after it is done, such how many good reads, how many bad reads, and how many reads are corrected.

Quality Control only

If you only want to get quality control statistics, run:

python after.py --qc_only

Understand the report

• AfterQC will generate a QC folder, which contains lots of figures.
• For pair-end sequencing data, both read1 and read2 figures will be in the same folder with the folder name of read1's filename. R1 means read1, R2 means read2.
• For single-end sequencing data, it will still have R1.
• prefilter means before filtering, postfilter means after filtering
• For pair-end sequencing data, After will do an overlap analysis. read1 and read2 will be overlapped when read1_length + read2_length > DNA_template_length.