IMAP – Chromosome-level Genome Assembler Combining multiple de novo Assemblies

IMAP

:: DESCRIPTION

IMAP (the integrative meta-assembly pipeline) is a new software pipeline to build chromosome-level genome sequence assemblies by generating and combining multiple initial assemblies using three de novo assemblers from short-read sequencing data.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • Python
  • Perl

:: DOWNLOAD

IMAP

:: MORE INFORMATION

Citation

PLoS One. 2019 Aug 27;14(8):e0221858. doi: 10.1371/journal.pone.0221858. eCollection 2019.
Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies.
Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang GI, Cherry JM, Kim J.

KeyPathwayMiner 5.0.1 – Combining networks with OMICS data

KeyPathwayMiner 5.0.1

:: DESCRIPTION

KeyPathwayMiner is not limited to analyses of single omics data sets, e.g. gene expression, but is able to directly combine several different omics data types.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 KeyPathwayMiner

:: MORE INFORMATION

Citation

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.
Alcaraz N, Pauling J, Batra R, Barbosa E, Junge A, Christensen AG, Azevedo V, Ditzel HJ, Baumbach J.
BMC Syst Biol. 2014 Aug 19;8:99. doi: 10.1186/s12918-014-0099-x.

Comb-p 0.43 – Combining, Analyzing, Grouping and Correcting Spatially Correlated P-values

Comb-p 0.43

:: DESCRIPTION

comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions.

::DEVELOPER

Katerina Kechris , Brent Pedersen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 Comb-p

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5.
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.
Pedersen BS1, Schwartz DA, Yang IV, Kechris KJ.

AgilePairedEndReadsCombiner 20140923 – Combining Paired End Read Data Sequences to form a Single Extended Read

AgilePairedEndReadsCombiner 20140923

:: DESCRIPTION

AgilePairedEndReadsCombiner reads a matching pair of fasta or fastq files created from a paired end sequence run which used PCR products as the library template and combines the data to produce a single read file contain data equivalent to the whole PCR product.

::DEVELOPER

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AgilePairedEndReadsCombiner

:: MORE INFORMATION