UrQt

UrQt an efficient software for NGS data quality trimming

Licence

UrQt is licensed under the General Public License v3 (GPLv3). The last version of this document is available in the UrQt website: https://lbbe.univ-lyon1.fr/-UrQt-.html

Installation Procedure :

You can directly clone the UrQt git repository:

git clone https://github.com/l-modolo/UrQt

or download the last version of UrQt: UrQt.1.0.17.tar.gz

wget ftp://pbil.univ-lyon1.fr/pub/logiciel/UrQt/UrQt.1.0.17.tar.gz
mkdir UrQt
tar xvzf UrQt.1.0.17.tar.gz -C UrQt

then compile it

cd UrQt
make

You can compile a static binary with the following commands:

make clean
make static

You should have a UrQt binary in your folder. Precompiled binary are also available here.

You may need to install zlib for UrQt to work/compile. For Ubuntu :

sudo apt-get install zlib1g-dev

Galaxy Installation Procedure :

With GALAYX_PATH the path to your galaxy distribution and after the compilation of UrQt.

You can install UrQt as a galaxy tools with the following commands :

mkdir GALAXY_PATH/tools/UrQt
cp UrQt UrQt.xml GALAXY_PATH/tools/UrQt/

and by appening the following line in a relevent section of the file GALAXY_PATH/config/tool_conf.xml :

<tool file="UrQt/UrQt.xml" />

Then restart the galaxy server You can edit the line 5 of the file UrQt.xml to adjust the number of core to use. Any modification to this file requiere a restart of the galaxy server.

Documentation

The last version of the documentation is available in the UrQt website: https://lbbe.univ-lyon1.fr/-UrQt-.html

UrQt (Unsupervised read Quality trimming) is a fast C++ software to trim nucleotides of unreliable quality from NGS data in fastq or fastq.gz format (automatically detected). For the phred score encoding, the default is 33 = Sanger (ASCII 33 to 126), but this can be modified with the option --phred to set for example 64 = Illumina 1.3 or 59 = Solexa/Illumina 1.0.

Single-end

To use UrQt on a single-end fastq of fastq.gz file simply run the following command:

UrQt --in file.fastq --out file_trimmed.fastq

Both input and output files must be accessible and writeable to UrQt to prevent errors.

Paired-end

To use UrQt on a paired-end fastq of fastq.gz file simply run the following command:

UrQt --in file_R1.fastq --inpair file_R2.fastq --out file_R2_trimmed.fastq --outpair file_R2_trimmed.fastq

By default UrQt remove empty reads (i.e. reads with zero nucleotides of good quality), and keep the correspondence between the paired-end files. Note that we recommend to use the option --gz and output your file in fastq.gz for significant gains of disk space.

Quality threshold

The quality threshold parameter --t threshold define the minimum phred score above which a phred score is considered as "good quality". By default UrQt use a phred of 5 but this can be changed with the option --t threshold. The classical definition of the quality threshold is obtained with --t 3.0103. Note that UrQt won’t remove every base with a phred score below --t, but will find the best segmentation between two segments of "bad quality" framing a segment of "good quality". This parameter is independent to the data and must be chosen according to the goal of the analysis.

Example to set a threshold of 10 :

UrQt --in file.fastq --out file_trimmed.fastq --t 10

Homopolymer trimming

With the option --N letter you can define the poly-nucleotide to trim at the head or tail of the sequences. For letters not present in the standard IUB/IUPAC dictionary, UrQt will perform QC trimming instead of poly-nucleotide trimming.

Example to trim polyA at the head and tail of the reads :

UrQt --in file.fastq --out file_trimmed.fastq --N A

Verbose mode

By default UrQt display a minimal number of information. If you want you can use the option --v to display all the options used, progress bars and time left.

UrQt --in file.fastq --out file_trimmed.fastq --v

Multi-threading

By default UrQt use 3 thread (main plus two sub-threads) for a total CPU usage of 100% of one processing unit. You can use the option --m thread_number to use more than one processing unit. Each additional thread will use a new processing unit.

To run UrQt on 10 processing units:

UrQt --in file.fastq --out file_trimmed.fastq --m 10

Head or Tail

By default, UrQt start by finding the best cut-point $k_1 \in [1,l]$ with $l$ the size of the read, between a segment of "good quality" and a segment of "bad quality", and then find the best cut-point $k_2 \in [1,k_1]$ between a segment of "bad quality" quality and a segment of "good quality". Instead of --pos both, one can use the parameter --pos head to only trim the head of the reads or --pos tail to only trim the tail of the reads.

Example to trim the head and tail of the reads :

UrQt --in file.fastq --out file_trimmed.fastq UrQt --in file.fastq --out file_trimmed.fastq --pos both

Example to trim only the head of the reads :

UrQt --in file.fastq --out file_trimmed.fastq --pos head

Example to trim only the tail of the reads :

UrQt --in file.fastq --out file_trimmed.fastq --pos tail

Minimum trimmed read size

You can tell UrQt to only report reads with a size superior to $n$ nucleotides with the option --min_read_size n Example to report only reads with a size superior to 15 nucleotides :

UrQt --in file.fastq --out file_trimmed.fastq --min_read_size 15

Maximum number of nucleotides trimmed

You can constrain UrQt to remove no more than n nucleotides at the tail of the reads with the option --max_tail_trim n. The complementary option for the head of the reads is --max_head_trim n.

Example to trim at maximum 10 nucleotides at the head of the reads :

UrQt --in file.fastq --out file_trimmed.fastq --max_head_trim 10

Example to trim at maximum 10 nucleotides at the tail of the reads :

UrQt --in file.fastq --out file_trimmed.fastq --max_tail_trim 10

Example to trim at maximum 10 nucleotides at the head and at the tail of the reads :

UrQt --in file.fastq --out file_trimmed.fastq --max_head_trim 10 --max_tail_trim 10

By default empty reads are removed from the output, you can keep them with the option --r.

Classical filter

You can tell UrQt to only keep reads with a minimum of $x$ percent of their length above y phred with the two following options: --min_QC_length x and --min_QC_phred y. This filter will be applied after the trimming procedure of UrQt.

For example to retain only reads with a phred of more than 20 on 80% of their length after trimming:

UrQt --in file.fastq --out file_trimmed.fastq --min_QC_length 80.0 --min_QC_phred 20

Nucleotides probability computation

By default, UrQt use the EM algorithm to compute the proportion of the 4 different nucleotides in a read and estimate the different cut-point. You can tell UrQt to use fixed proportion of $1/4$ for each nucleotides with the option --S. To compute the proportion of each nucleotide on a sample of size n reads, you can use the option --s n. These two option speed-up the computation but we recommend to use the default parameters (no parameter) for a better estimate of the cut-points in the reads.