PBSIM 1.0.3 – PacBio Reads Simulator

PBSIM 1.0.3

:: DESCRIPTION

PacBio sequencers produced two types of characteristic reads: CCS (short and low error rate) and CLR (long and high error rate), both of which could be useful for de novo assembly of genomes. PBSIM simulates those PacBio reads by using either a model-based or sampling-based simulation.

::DEVELOPER

Yukiteru Ono ,Kiyoshi Asai ,Michiaki Hamada

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PBSIM

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jan 1;29(1):119-21. doi: 10.1093/bioinformatics/bts649.
PBSIM: PacBio reads simulator–toward accurate genome assembly.
Ono Y, Asai K, Hamada M.

proovread 2.14.1 – Large-scale high accuracy PacBio Correction through iterative Short Read Consensus.

proovread 2.14.1

:: DESCRIPTION

proovread is a hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high performance computing cluster.

::DEVELOPER

Department of Bioinformatics, University of Würzburg,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
SHRiMP2
bash version 4 or above

:: DOWNLOAD

proovread

:: MORE INFORMATION

Citation:

proovread: large-scale high accuracy PacBio correction through iterative short read consensus.
Hackl T, Hedrich R, Schultz J, Förster F.
Bioinformatics. 2014 Jul 10. pii: btu392.

InDelFixer 1.1 – An Insertion and Deletion Fixing Aligner for 454, Illumina and PacBio

InDelFixer 1.1

:: DESCRIPTION

InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

InDelFixer

:: MORE INFORMATION

PaSS – A PacBio Sequencing Simulator

PaSS

:: DESCRIPTION

PaSS is a fast sequencing simulator for PacBio sequencing with a high fidelity. It will facilitate the evaluation and development of new analysis tools for the PacBio sequencing data.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

PaSS

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2019 Jun 21;20(1):352. doi: 10.1186/s12859-019-2901-7.
PaSS: a sequencing simulator for PacBio sequencing.
Zhang W, Jia B, Wei C

LoRDEC 0.9 – A Hybrid Error Correction program for long, PacBio Reads

LoRDEC 0.9

:: DESCRIPTION

LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GATB library

:: DOWNLOAD

LoRDEC

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Aug 26. pii: btu538.
LoRDEC: accurate and efficient long read error correction.
Salmela L, Rivals E.