MetaAnnotator
MetaAnnotator is a novel software for binning and annotating short paired-end reads.
(1) Use a novel annotating method;
(2) Incorporate different reference databases;
(2) Annotate more accurately, comparing to existing tools e.g MEGAN5, TANGO and MetaCluster-TA;
(4) Cost much less time.
(1) Use a novel annotating method;
(2) Incorporate different reference databases;
(2) Annotate more accurately, comparing to existing tools e.g MEGAN5, TANGO and MetaCluster-TA;
(4) Cost much less time.
*Usage&Requirement(download)
MetaCluster-TA
MetaCluster-TA is a new software for binning and annotating short paired-end reads.
(1) improved clustering/binning performance, comparing to MetaCluster5.0;
(2) more annotated reads and more accurate annotation, comparing to MEGAN4;
*Usage information can be found in README file in the package(see in download tab).
(1) improved clustering/binning performance, comparing to MetaCluster5.0;
(2) more annotated reads and more accurate annotation, comparing to MEGAN4;
*Usage information can be found in README file in the package(see in download tab).
MetaCluster 5.0
MetaCluster5.0 is an unsupervised binning method that can
(1) samples with low-abundance species, or
(2) samples (even with high-abundance) with many extremely-low-abundance species.
(1) samples with low-abundance species, or
(2) samples (even with high-abundance) with many extremely-low-abundance species.
Release Package Information
The version 5.0.1 release
package contains the C++ source code of "MetaCluster 5.0 version". Download from
here.
Runtime Environment
This software is suitable for all unix-like 64-bit system with gcc installed.
It is not necessary but highly recommanded to install openmp for muilt-cpu machine.
Compile
Code
1.Extract the package.
2.Use the command :
$ ./configure
$ make
3.After compiling, the tools 'MetaCluster5_1' & 'MetaCluster5_2' are in the directory: ./bin
2.Use the command :
$ ./configure
$ make
3.After compiling, the tools 'MetaCluster5_1' & 'MetaCluster5_2' are in the directory: ./bin
Command Format
Please refer to the README file in the package.
MetaCluster 4.0.6 version
MetaCluster4.0 is an unsupervised binning method that can
(1) deal with short reads(75bp),
(2) deal with species of similar abundance ratios as well as extreme ratios,
(3) determine the number of species automatically, and
(4) have acceptable performance even when the species number is much larger than 10.
(1) deal with short reads(75bp),
(2) deal with species of similar abundance ratios as well as extreme ratios,
(3) determine the number of species automatically, and
(4) have acceptable performance even when the species number is much larger than 10.
Release Package Information
The version 4.0.6 release
package contains the C++ source code of "MetaCluster 4.0.6". Download from
here.
Runtime Environment
This software is suitable for all unix-like 64-bit system with gcc installed.
It is not necessary but highly recommanded to install openmp for muilt-cpu machine.
Compile
Code
1.Extract the package.
2.Use the command :
$ ./configure
$ make
3.After compiling, the tool 'MetaCluster4' is in the directory: ./bin
2.Use the command :
$ ./configure
$ make
3.After compiling, the tool 'MetaCluster4' is in the directory: ./bin
Command Format
The typical command format of MetaCluster 4 is:
MetaCluster4 input-file [options]
For the details of [options], please refer to the README file in the package.
Input & Output
The input of MetaCluster 4 should be in fasta format.
Every odd-number read and its next read are supposed to be pair-end reads.
The default format output file is FATSA file with binning-label, e.g.:
Cluster : 0
>read2_35/1
>read2_35/2
>read2_96/1
>read2_96/2
Cluster : 1
>read1_10/1
>read1_10/2
>read1_55/1
>read1_55/2
MetaCluster 3.0
MetaCluster 3.0 is an unsupervised binning method for
metagenomic sequences.Existing binning methods based on sequence similarity
and sequence composition markers rely heavily on the reference genomes of
known microorganisms and phylogenetic markers. While MetaCluster 3.0 is an
integrated binning method based on the unsupervised top-down separation and
bottom-up merging strategy. It can bin metagenomic sequencing datasets with
mixed complex species abundance ratios from the exactly equal situation to
the extremely unbalance situation with consistently higher accuracy when
compared with other recently reported methods.
Release Package Information
The version 3.0 release
package contains the C++ source code of "MetaCluster 3.0". Download from
here.
Runtime Environment
64-bit processor and 1G or
more memory is highly recommended for better performance or solving large
dataset. MetaCluster 3.0 is developed and tested under Ubuntu 10.04 64bit
version and Debian 6.0 64bit version and should be suitable for all Linux
environments.
Compile
Code
1.Decompress the package.
2.Use the command :
#make
So that files will be compiled.
3.After compiling, the tools 'metaCluster-3.0' is in the directory: /bin
2.Use the command :
#make
So that files will be compiled.
3.After compiling, the tools 'metaCluster-3.0' is in the directory: /bin
Command Format
The typical command format of MetaCluster 3.0 is:
metacluster input-file
[--threshold]
input-file:
The input file you want to bin. This is the compulsory parameter.
[--threshold]:
The threshold for
the bottom-up merge step. The default value for t is 0.9.
Input & Output
The input of MetaCluster 3.0 should be a sequencing dataset, say test.fa, contains several DNA fragments with FASTA format, e.g.
>read0001
TACGCGGACTTCGATGCG
GCTAGGCTGACG
GCTAGGCTGACG
>read0002
GCCTGCGAAGCGCGATTT
AGCTGAGGCGTC
AGCTGAGGCGTC
The default format output files only contain the FATSA comments, e.g.:
>read0001
>read0002
Samples
metaCluster-3.0
test.fa
metaCluster-3.0 test.fa --threshold 0.83
metaCluster-3.0 test.fa --threshold 0.83
Copyright 2010-2014, Department of Computer Science, The University of Hong Kong. & Mr. WANG YI
MetaAnnotator beta version is released!
If you have any questions, please contact ywang@cs.hku.hk
