OpenGene/defq

Name: defq

Owner: OpenGene - Open Source Genetics Toolbox

Description: Ultra-fast Multi-threaded FASTQ Demultiplexing (in dev)

Created: 2017-12-06 00:32:18.0

Updated: 2018-01-04 01:10:59.0

Pushed: 2017-12-06 10:18:11.0

Homepage:

Size: 508

Language: C

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

User	Email	Most Recent Commit	# Commits

README

defq

Ultra-fast Multi-threaded FASTQ Demultiplexing

introduction

Use either index1 or index2 to demultiplex a single FASTQ file to multiple FASTQ files. This tool is developed in C++ with multi-threading supported.

simple usage

ad1 and read2 are precessed separately
 specifies the output folder, and current working directory is used by default
 specifies the filename suffix so that R1 / R2 can have different file name
 specifies a samplesheet to defq how to demux
 -i in.R1.fq -o demux_out_dir -s samplesheet.csv -f .R1.fq
 -i in.R2.fq -o demux_out_dir -s samplesheet.csv -f .R2.fq

Where samplesheet.csv is 3-column (filename, index1, index2) CSV file. You can use index1 for all samples, or use index2 for all samples, but you cannot use both index1 and index2. If the indexes have different length, defq will match the longer index first, and then match the shorter ones if the read is still not matched. A sample sheet example:

ename, #index1, #index2
1, ATTCAGAA,
2, ATTACT,
3, GAGATTCC,
4, CGCTCATT,

You will then have following output:

x_out_dir/
Undetermined.R1.fq
Undetermined.R2.fq
file1.R1.fq
file1.R2.fq
file2.R1.fq
file2.R2.fq
file3.R1.fq
file3.R2.fq
file4.R1.fq
file4.R2.fq

get defq

compile from source

t source (you can also use browser to download from master or releases)
clone https://github.com/OpenGene/defq.git

ild
efq


stall
 make install

gzip compression

When the output file name is ended with .gz, the output will be compressed with gzip.

• If you specify file name suffix by -f or --suffix1, add .gz into the suffix.
• If you don't specify file name suffix by -f or --suffix1, add .gz into the file name column in samplesheet.csv.

all options

e: defq --in1=string --sample_sheet=string [options] ... 
ons:
, --in1             input file name (string)
, --sample_sheet    a CSV file contains three columns (filename, index1, index2) (string)
, --out_folder      output folder, default is current working directory (string [=.])
, --suffix1         the suffix to be appended to the output file name given in sample sheet, default is none (string [=])
, --undetermined    the file name of undetermined data, default is Undetermined (string [=Undetermined])
, --compression     compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 2. (int [=2])
, --help            print this message