PERGA 0.5.03.02 – Paired End Reads Guided Assembler

PERGA 0.5.03.02

:: DESCRIPTION

PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds.

::DEVELOPER

PERGA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PERGA

:: MORE INFORMATION

Citation

PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach.
Zhu X, Leung HC, Chin FY, Yiu SM, Quan G, Liu B, Wang Y.
PLoS One. 2014 Dec 2;9(12):e114253. doi: 10.1371/journal.pone.0114253.

CAGEScan-Clustering 1.2 – Create CAGEscan Clusters from CAGE paired-end reads

CAGEScan-Clustering 1.2

:: DESCRIPTION

CAGEScan-Clustering creates transcript assemblies from CAGEScan derived Transcription Start Site (TSS) associated reads paired with randomly primed readsm, grouping them on the basis of the common location of TSS reads.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl
BedTools v2.9.0 or higher

:: DOWNLOAD

CAGEScan-Clustering

:: MORE INFORMATION

Skewer 0.2.2 – Adapter Trimmer for Next-generation Sequencing Paired-end Reads

Skewer 0.2.2

:: DESCRIPTION

Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.

::DEVELOPER

Hongshan Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Skewer

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182.
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
Jiang H, Lei R, Ding SW, Zhu S