<<<<<<< HEAD
ReadTrim is a workflow that I use for NGS reads trimming and QC. The ReadTrim is open source and released under the GNU General Public License (Version 3).
Installation and usage refer to document
Install readtrim through pip3:
pip3 install readtrim
For any bugs or problems please use Issue portal.
Copyright 2018-2019 Jie Li. See LICENSE for further details.
This repo was archived, it has been integrated into ReadTrim.
FastQC is a module which used for Illumina raw sequencing data QC.
This repo was archived, is has been integrated into ReadTrim.
Filter_Trimmomatic is a module which used for Illumina raw sequencing data QC and trimming.
No need to install, just clone and then use it.
Use FastQC to process raw reads, do FastQC of sequencing reads
--fqlist fqlist file, with header, sampleNameq1q2, abs path --adapters adapters, format nameadapter seq --outdir outdir to output result, default is ./ --qsubs arguments for qsub system, [select=1:ncpus=2:mem=2GB] --walltime walltime of your task to run [00:60:00] --run set if you want to run all scripts directly. --arguments other arguments you want to use for FastQC --rm set to rm .sh. files
This is a demo of usage python3 fastQC-v1.0.py --fqlist fq.list --outdir ./test
Use Trimmomatic to process raw reads, Use seqtk to stat and process clean reads, then you get high quality PE reads.
--rawData_list raw reads list file with header,SampleNameFQ1FQ2Adapter,if you want to merge fq1s then, SampleNamefq1,fq1fq2,fq2Adapter, if you have two adps, then name\tq1\tq2\ta1,a2 --read_length raw read length, [100] --sliding_window windowSize:average_quality_required, [4:20] --phred phred, 33 or 64, [33] --adapters adapters sequences file --adapters_paras params for adapters, seedMismatchs:palindromeClipThreshold:simpleClipThreshold [2:30:10] --duplicates set if you want to remove duplicates
This is a demo of usage python3 Filter_trimmomatic-1.2.py --rawData_list fq_DNA.list --read_length 151 --minlength 75 --phred 33 --adapters adapters.txt --sliding_window 6:20 --outdir /home/1.Filter
Copyright 2017-2018 Jie Li. See LICENSE for further details.
QC raw sequencing reads, filter and trim low quality reads, remove duplications, generate stats file, and then QC again.