Description

Program SeqyClean Version: 1.10.09 (2017-10-16)

Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.

SeqyClean offers:

• Adapter/key/primers filtering
• Vector and contaminants filtering.
• Quality trimming.
• Poly A/T trimming.
• Overlapping paired reads.

It handles SFF and FASTQ file formats.

Prerequisites

Developer version of the zlib:

$sudo apt-get install zlib1g-dev

Installation

Clone or download the repository. Then cd to seqyclean home folder, and type make.

Note: by default, it builds the binary for OS-X. It should build on Linux as well. If not, try to use this command:

make PLATFORM=-DLINUX

or simply contact me: ilya.zhbannikov@duke.edu

Usage

usage: ./seqyclean libflag input_file_name_1 [libflag input_file_name_2] -o output_prefix [options]

The parameter libflag here is a library type: -454 for Roche 454 reads, -1, -2 for paired-end Illumina reads, -U for single-end reads. See examples below.

Common arguments for all library types

-h, --help - Show this help and exit.
-v <filename> - Turns on vector trimming, default=off. <filename> - is a path to a FASTA-file containing vector genomes.
-c <filename> - Turns on contaminants screening, default=off, <filename> - is a path to a FASTA-file containing contaminant genomes.
-k <value> - Common size of k-mer, default=15.
-d - Distance between consecutive k-mers, default=1.
-kc <value> - Size of k-mer used in sampling contaminat genome, default=15.
-qual ```max_average_error max_error_at_ends``` - Turns on quality trimming, default=off. Error boundaries: max_average_error (default=20 Phred), max_error_at_ends (default=20 Phred).
-braket ```window_size max_average_error``` - Parameter for quality trimming. By default window_size=10 and max_average_error=0.794.
-window ```window_size max_average_error``` [```window_size maximum_average_error``` [...]] - Parameters for quality trimming. By default there are two windows with size of 50 and 10 bp with the same max_average_error=0.794.
-ow - Overwrite existing results, default=off.
-minlen <value> - Minimum length of read to accept, default=100 bp.
-polyat [cdna] [cerr] [crng] - Turns on poly A/T trimming, default=off. Parameters: cdna (default=10) - maximum size of a poly tail, cerr (default=3) - maximum number of G/C nucleotides within a tail, cnrg (default=50) - range to look for a tail within a read.
-verbose - Verbose output, default=off.
-detrep - Generate detailed report for each read, default=off.
-dup [-startdw][-sizedw][-maxdup] - Turns on screening duplicated sequences, default=off. Here startdw (defalt=10) and sizedw (default=35) are starting position and size of the window within a read, -maxdup (default=3) - maximum number of duplicated sequences allowed.
-no_adapter_trim - Turns off adapter trimming, default=off.

Roche 454 arguments

-t <value> - Number of threads (not yet applicable to Illumina mode), default=4.
-fastq - Output in FASTQ format, default=off.
-fasta - Output in FASTA format, default=off.
-m <filename> - Using custom barcodes, default=off. <filename> - a path to a FASTA-file with custom barcodes.

Illumina paired- and single-end arguments

-1 <filename1> -2 <filename2> - Paired-end mode (see examples below)
-U <filename> - Single-end mode
-shuffle - Store non-paired Illumina reads in shuffled file, default=off.
-i64 - Turns on 64-quality base, default = off.
-adp <filename> - Turns on using custom adapters, default=off. <filename> - FASTA file with adapters
-at <value> - This option sets the similarity threshold for adapter trimming by overlap (only in paired-end mode). By default its value is set to 0.75.
-overlap <value> - This option turns on merging overlapping paired-end reads and <value> is the minimum overlap length. By default the minimum overlap length is 16 base pairs.
-new2old - A switch to fix read IDs, default=off ( As is detailed in: http://contig.wordpress.com/2011/09/01/newbler-input-iii-a-quick-fix-for-the-new-illumina-fastq-header/#more-342 ).
-gz - A flag that indicates compressed (.gz) output, default=off.
-alen - Maximum adapter length, default=30 bp.(only for paired-end mode).

###Please note We call 'Adapter' for Illumina reads the thing, which contains: [Adapter P5/P7 + Index I5/I7 + Linker (primer hybridization)]. In other words 'Adapter' the total foreign sequence attached to 5' or 3' end of the piece of DNA.

Examples

Roche 454

Output in SFF, no quality trimming, vector trimming is performed:

./seqyclean -454 test_data/in.sff -o test/Test454 -v test_data/vectors.fasta

Output in SFF, quality trimming with default parameters, vector trimming and contaminants screening are performed:

./seqyclean -454 test_data/in.sff -o test/Test454 -qual -v test_data/vectors.fasta -c test_data/contaminants.fasta

Illumina

Paired-end

Trimming of adapters is performed, quality trimming with default parameters:

./seqyclean -1 test_data/R1.fastq.gz -2 test_data/R2.fastq.gz -qual -o test/Test_Illumina

Trimmings of adapters and vectors are performed, quality trimming with default parameters:

./seqyclean -1 test_data/R1.fastq.gz -2 test_data/R2.fastq.gz -qual -v test_data/vectors.fasta -o test/Test_Illumina

Single-end

Trimming of adapters, vectors and contaminant screening are performed, quality trimming with default parameters:

./seqyclean -U test_data/R1.fastq.gz -o test/Test_Illumina -v test_data/vectors.fasta -c test_data/contaminants.fasta
                                

Citing SeqyClean

BibText

@inproceedings{Zhbannikov:2017:SPH:3107411.3107446,
 author = {Zhbannikov, Ilya Y. and Hunter, Samuel S. and Foster, James A. and Settles, Matthew L.},
 title = {SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing},
 booktitle = {Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics},
 series = {ACM-BCB '17},
 year = {2017},
 isbn = {978-1-4503-4722-8},
 location = {Boston, Massachusetts, USA},
 pages = {407--416},
 numpages = {10},
 url = {http://doi.acm.org/10.1145/3107411.3107446},
 doi = {10.1145/3107411.3107446},
 acmid = {3107446},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {data preprocessing, high-throughput dna sequencing, sequence analysis},
} 

Plain text (ACM Ref)

Ilya Y. Zhbannikov, Samuel S. Hunter, James A. Foster, and Matthew L. Settles. 2017. SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics (ACM-BCB '17). ACM, New York, NY, USA, 407-416. DOI: https://doi.org/10.1145/3107411.3107446

EndNote

%0 Conference Paper
%1 3107446
%A Ilya Y. Zhbannikov
%A Samuel S. Hunter
%A James A. Foster
%A Matthew L. Settles 
%T SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing
%B Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics
%@ 978-1-4503-4722-8
%C Boston, Massachusetts, USA
%P 407-416
%D 2017
%R 10.1145/3107411.3107446
%I ACM

Contacts

Please ask Ilya (ilya.zhbannikov@duke.edu) in case of any questions.