jsPISA 2.0.4 – Protein Interfaces, Surfaces and Assemblies

jsPISA 2.0.4

:: DESCRIPTION

jsPISA is an interactive web tool for the calculation of macromolecular surfaces and interfaces, assessment of their properties and inference on probable macromolecular assemblies (complexes) from coordinate data, typically delivered by crystallographic X-ray experiment.

:: DEVELOPER

Eugene Krissinel ( eugene.krissinel@stfc.ac.uk.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Apr 23. pii: gkv314.
Stock-based detection of protein oligomeric states in jsPISA.
Krissinel E

Compartmentalized Assembler – Assembly of Physical Maps

Compartmentalized Assembler

:: DESCRIPTION

Compartmentalized assembler is a novel method for the assemlby of high quality physical maps from fingerprinted clones.

::DEVELOPER

Bozdag Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Compartmentalized assembler

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jul 15;10:217. doi: 10.1186/1471-2105-10-217.
A compartmentalized approach to the assembly of physical maps.
Bozdag S1, Close TJ, Lonardi S.

Atlas 2005 – Whole Genome Assembly Suite

Atlas 2005

:: DESCRIPTION

Atlas is a collection of software tools to facilitate the assembly of large genomes from whole genome shotgun reads, or a combination of whole genome shotgun reads and BAC or other localized reads.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Atlas

:: MORE INFORMATION

PathRacer 3.15.0 – Racing Profile HMM Paths on Assembly Graph

PathRacer 3.15.0

:: DESCRIPTION

PathRacer is a novel standalone tool that aligns profile HMM directly to the assembly graph (performing the codon translation on fly for amino acid pHMMs). The tool provides the set of most probable paths traversed by a HMM through the whole assembly graph, regardless whether the sequence of interested is encoded on the single contig or scattered across the set of edges, therefore significantly improving the recovery of sequences of interest even from fragmented metagenome assemblies.

::DEVELOPER

Center for Algorithmic Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python

:: DOWNLOAD

PathRacer

:: MORE INFORMATION

WhatsHap – Haplotype Assembly for Future-Generation Sequencing Reads

WhatsHap

:: DESCRIPTION

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

::DEVELOPER

The Algorithms for Computational Genomics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
C++

:: DOWNLOAD

WhatsHap

:: MORE INFORMATION

Citation

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.
J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157

PyRAD 3.0.66 – Assembly of de novo RADseq loci for Phylogenetic Analyses

PyRAD 3.0.66

:: DESCRIPTION

PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
Python

:: DOWNLOAD

PyRAD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 20.
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses.
Eaton DA.

CEM 0.9.1 – Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads

CEM 0.9.1

:: DESCRIPTION

CEM is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

CEM

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2914-21. doi: 10.1093/bioinformatics/bts559. Epub 2012 Oct 11.
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
Li W1, Jiang T.

MetaCompass 1.0 – Comparative Assembly of Metagenomic Sequences

MetaCompass 1.0

:: DESCRIPTION

MetaCompass is a software package for comparative assembly of metagenomic reads. MetaCompass achieves comparable assembly performance to the state of the art de novo assemblers, but these two different approaches complement each other a lot. So combining contigs between MetaCompass and other independent de novo assemblers give us the best overall metagenomic assembly.

::DEVELOPER

MetaCompass team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
BLAST
Bowtie 2
Perl

:: DOWNLOAD

MetaCompass

:: MORE INFORMATION

Telescoper 0.2 – De novo Assembly Algorithm

Telescoper 0.2

:: DESCRIPTION

Telescoper is a local assembly algorithm designed for short-reads from NGS platforms such as Illumina. The reads must come from two libraries: one short insert, and one long insert.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Telescoper

:: MORE INFORMATION

Citation

Bresler, M., Sheehan, S., Chan, A.H., and Song, Y.S.
Telescoper: De novo Assembly of Highly Repetitive Regions.
Bioinformatics, 28 (2012) i311-i317.

laSV 1.0.2 – Local Assembly based Structural Variation Discovery tool

laSV 1.0.2

:: DESCRIPTION

laSV is a software that employs a local de novo assembly based approach to detect genomic structural variations from whole-genome high-throughput sequencing datasets.

::DEVELOPER

ZLab, University of Massachusetts Medical School, Worcester, MA, USA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

laSV

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Sep 30;43(17):8146-56. doi: 10.1093/nar/gkv831. Epub 2015 Aug 17.
Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.
Zhuang J, Weng Z