Difference between revisions of "MetaCluster"

Revision as of 18:40, 15 November 2012

Description

metacluster website
MetaCluster 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. MetaCluster 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.

Required Modules

modules documentation

Serial

metacluster

System Variables

HPC_{{#uppercase:metacluster}}_DIR - installation directory
HPC_HTSEQ_BIN - executable directory.

Additional Information

Two programs are available - htseq-count and htseq-qa. Run them without any arguments to see the usage information. The main HTSeq module can be loaded from python (import HTSeq). See HTSeq documentation for a tutorial.

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
 {|<!--Main settings - REQUIRED-->
 |{{#vardefine:app|metacluster}}
-|{{#vardefine:url|__NOTOC__
+|{{#vardefine:url|http://i.cs.hku.hk/~alse/MetaCluster/index.html}}
-__NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
-{|<!--Main settings - REQUIRED-->
-|{{#vardefine:app|fasta}}
-|{{#vardefine:url|http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml}}
 |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 22: / Line 17: @@
 {{#if: {{#var: url}}|
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
+MetaCluster 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. MetaCluster 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.
-The FASTA programs find regions of local or global (new) similarity between
-Protein or DNA sequences, either by searching Protein or DNA databases, or
-by identifying local duplications within a sequence. Other programs provide
-information on the statistical significance of an alignment. Like BLAST,
-FASTA can be used to infer functional and evolutionary relationships between
-sequences as well as help identify members of gene families.
 <!--Modules-->
 ==Required Modules==
@@ Line 36: / Line 26: @@
 ==System Variables==
 * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
-* HPC_FASTA_BIN - executable directory
+* HPC_HTSEQ_BIN - executable directory.
-==Available documentation==
+<!--Additional-->
-Several man pages are available:
+{{#if: {{#var: exe}}|==Additional Information==
-* fasta3, fastf3, fasts3, map_db, prss3, pvcomp
+Two programs are available - htseq-count and htseq-qa. Run them without any arguments to see the usage information. The main HTSeq module can be loaded from python (import HTSeq). See HTSeq documentation for a tutorial.
-Type "man MANPAGE" to access them at the command line.
-{{#if: {{#var: conf}}|==Configuration==
-See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
-{{#if: {{#var: pbs}}|==PBS Script Examples==
-See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage Policy==
-WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
-{{#if: {{#var: testing}}|==Performance==
-WRITE PERFORMANCE TESTING RESULTS HERE|}}
-{{#if: {{#var: faq}}|==FAQ==
-*'''Q:''' **'''A:'''|}}
-{{#if: {{#var: citation}}|==Citation==
-If you publish research that uses {{{app}}} you have to cite it as follows:
-WRITE CITATION HERE
 |}}
-}}
-|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
-|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
-|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
-|{{#vardefine:policy|}} <!--Enable policy section -->
-|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
-|{{#vardefine:faq|}} <!--Enable FAQ section -->
-|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
-|}
-<!-- ########  Template Body ######## -->
-<!--Description-->
-{{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-The FASTA programs find regions of local or global (new) similarity between
-Protein or DNA sequences, either by searching Protein or DNA databases, or
-by identifying local duplications within a sequence. Other programs provide
-information on the statistical significance of an alignment. Like BLAST,
-FASTA can be used to infer functional and evolutionary relationships between
-sequences as well as help identify members of gene families.
-<!--Modules-->
-==Required Modules==
-[[Modules|modules documentation]]
-===Serial===
-*{{#var:app}}
-==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
-* HPC_FASTA_BIN - executable directory
-==Available documentation==
-Several man pages are available:
-* fasta3, fastf3, fasts3, map_db, prss3, pvcomp
-Type "man MANPAGE" to access them at the command line.
 {{#if: {{#var: conf}}|==Configuration==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}