I appreciate hearing about your experience with the matemaker.
matemaker will generate a pair of fastq files (left and right) that
consist of artificial mate-pairs generated from one or more sequences sent
in as input. It is intended to scaffold an optimal assembly with suboptimal
assemblies. The generated matepairs are in the same orientation as illumina matepair sequencing, and can be used without modification as input to any scaffolding software that accepts illumina mate-pairs (e.g., SSPACE). Quality scores are all set to unknown (represented by the character 'B').
I recommend running the program multiple times with an array of insert sizes. See examples.
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https://github.com/josephryan/matemaker (click the "Download ZIP" button at the bottom of the right column).
General system tools:
- [Perl] (http://www.cpan.org/), comes with most operating systems
Additional package
- JFR-PerlModules - https://github.com/josephryan/JFR-PerlModules
To install matemaker and documentation, type the following:
perl Makefile.PL
make
sudo make install
If you do not have permission to install to the system see the following:
http://www.perlmonks.org/index.pl?node_id=128077#permission
matemaker --assembly=ASSEMBLY.fa --out=PREFIX
In the examples directory there are 2 files:
Hsap.chr22.opt.fa - (N50: 5000000)
Human Chromosome 22 divided into chunks of size 5000000
Hsap.chr22.subopt.fa - (N50: 1000000)
Human Chromosome 22 divided into chunks of size 1000000
The first 25000000 NTs (of which all were N) were removed to create
an offset of breakpoints with Hsap.chr22.opt.fa
To create matepairs try:
matemaker --assembly=Hsap.chr22.subopt.fa --insertsize=2000 --out=chr22.2000
matemaker --assembly=Hsap.chr22.subopt.fa --insertsize=5000 --out=chr22.5000
matemaker --assembly=Hsap.chr22.subopt.fa --insertsize=10000 --out=chr22.10000
The resulting files are:
chr22.2000.A.fq, chr22.2000.B.fq
chr22.5000.A.fq, chr22.5000.B.fq
chr22.10000.A.fq, chr22.10000.B.fq
These can be used as input to a scaffolding software (e.g., SSPACE) to scaffold the optimal assembly:
Hsap.chr22.opt.fa
matemaker --assembly assembly.fa --insertsize=1000 --out=01k
matemaker --assembly assembly.fa --insertsize=2000 --out=02k
matemaker --assembly assembly.fa --insertsize=3000 --out=03k
matemaker --assembly assembly.fa --insertsize=4000 --out=04k
matemaker --assembly assembly.fa --insertsize=5000 --out=05k
matemaker --assembly assembly.fa --insertsize=6000 --out=06k
matemaker --assembly assembly.fa --insertsize=7000 --out=07k
matemaker --assembly assembly.fa --insertsize=8000 --out=08k
matemaker --assembly assembly.fa --insertsize=9500 --out=09k
matemaker --assembly assembly.fa --insertsize=10000 --out=10k
matemaker --assembly assembly.fa --insertsize=11000 --out=11k
matemaker --assembly assembly.fa --insertsize=12000 --out=12k
matemaker --assembly assembly.fa --insertsize=13000 --out=13k
matemaker --assembly assembly.fa --insertsize=14000 --out=14k
matemaker --assembly assembly.fa --insertsize=15000 --out=15k
matemaker --assembly assembly.fa --insertsize=16000 --out=16k
matemaker --assembly assembly.fa --insertsize=17000 --out=17k
matemaker --assembly assembly.fa --insertsize=18000 --out=18k
matemaker --assembly assembly.fa --insertsize=19500 --out=19k
matemaker --assembly assembly.fa --insertsize=20000 --out=20k
matemaker --assembly assembly.fa --insertsize=21000 --out=21k
matemaker --assembly assembly.fa --insertsize=22000 --out=22k
matemaker --assembly assembly.fa --insertsize=23000 --out=23k
matemaker --assembly assembly.fa --insertsize=24000 --out=24k
matemaker --assembly assembly.fa --insertsize=25000 --out=25k
matemaker --assembly assembly.fa --insertsize=26000 --out=26k
matemaker --assembly assembly.fa --insertsize=27000 --out=27k
matemaker --assembly assembly.fa --insertsize=28000 --out=28k
matemaker --assembly assembly.fa --insertsize=29500 --out=29k
matemaker --assembly assembly.fa --insertsize=30000 --out=30klib1 bwa 01k.A.fq 01k.B.fq 1000 0.25 RF
lib2 bwa 02k.A.fq 02k.B.fq 2000 0.25 RF
lib3 bwa 03k.A.fq 03k.B.fq 3000 0.25 RF
lib4 bwa 04k.A.fq 04k.B.fq 4000 0.25 RF
...
lib27 bwa 27k.A.fq 27k.B.fq 27000 0.25 RF
lib28 bwa 28k.A.fq 28k.B.fq 28000 0.25 RF
lib29 bwa 29k.A.fq 29k.B.fq 29500 0.25 RF
lib30 bwa 30k.A.fq 30k.B.fq 30000 0.25 RFDocumentation is embedded inside of matemaker in POD format and
can be viewed by running any of the following:
matemaker --help
perldoc matemaker
man matemaker # available after installation
--assembly
The FASTA file with the sequence or sequences from which to generate
the mates
--out
A prefix to use for the output FASTQ (or FASTA) files
--readlen
(default: 50) the read length of the produced mate-pair library
--insertsize
(default: 5000) the length of the insert size of the produced mate-
pair library
--fasta
by default matepairs are created in fastq format, but with this
option they can be made as fasta files
--print_inserts
this option will generate an additional output file that includes the
full sequences of the inserts that were used to create the mate-pairs
--print_coords
this option will generate an additional output file (csv format) that
includes the mate_pair id, the coordinates of the mates and the
sequence_id of the sequence used to create the mates. The suffix
will be `coords.csv` and the format of the file is:
mate_id,mate1_coord,mate2_coord,defline_of_seq_used_to_generate_mate
--matesperkb
(default: 5) the number of mates randomly generated for a particular
sequence follows the formula ( (SEQUENCE_LENGTH - INSERTSIZE) / (1000
/ MATESPERKB) )
Copyright (C) 2015 Joseph F. Ryan
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program in the file LICENSE. If not, see http://www.gnu.org/licenses/.