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

PASS 2.28 – Align Short Sequences

PASS 2.28

:: DESCRIPTION

PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of “seed” words (typically 11-12 bases) as well as an index of the precomputed scores of short words (typically 7-8 bases) aligned against each other.

::DEVELOPER

Davide Campagna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASS

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jan 15;29(2):268-70. doi: 10.1093/bioinformatics/bts675. Epub 2012 Nov 17.
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Campagna D1, Telatin A, Forcato C, Vitulo N, Valle G.

Bioinformatics. 2009 Apr 1;25(7):967-8. Epub 2009 Feb 13.
PASS: a program to align short sequences.
Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G.

PASS 2 – Control the FDR level in ChIP data analysis

PASS 2

:: DESCRIPTION

PASS (Poisson Approximation for Statistical Significance) is a software that can accurately control the FDR level in ChIP data analysis. The method is designed for detecting transcription factor binding, and may not work well for wide spread signals such as nucleopositioning data. If the data is from ChIP-seq, you need to convert each ChIP-seq value into z-scores before using this program.

::DEVELOPER

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASS

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Dec 15;24(24):2825-31. Epub 2008 Oct 25.
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays.
Zhang Y.