VERSE v1.0.5 – Versatile and Efficient RNA-Seq Read Counting Tool

VERSE v1.0.5

:: DESCRIPTION

VERSE is designed for high-performance read summarization for next generation sequencing. VERSE is 50x faster than HTSeq when computing the same gene counts. It introduces a novel, hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. There is also a set of parameters the user can use to fine-tune the assignment logic. VERSE can be readily incorporated into any existing RNA-Seq analysis pipelines.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

VERSE 

:: MORE INFORMATION

Citation

Zhu, Q., Fisher, S.A., Shallcross, J., Kim, J. (Preprint).
VERSE: a versatile and efficient RNA-Seq read counting tool. bioRxiv 053306.
doi: http://dx.doi.org/10.1101/053306

ganon 1.0.0 – Read Classification tool based on Interleaved Bloom Filters

ganon 1.0.0

:: DESCRIPTION

ganon is a k-mer based DNA classification tool using Interleaved Bloom Filters for short reads.

::DEVELOPER

Vitor C. Piro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ganon

:: MORE INFORMATION

Citation

Piro VC, Dadi TH, Seiler E, Reinert K, Renard BY.
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences.
Bioinformatics. 2020 Jul 1;36(Suppl_1):i12-i20. doi: 10.1093/bioinformatics/btaa458. PMID: 32657362; PMCID: PMC7355301.

Rcount – Simple and Flexible RNA-Seq Read Counting

Rcount

:: DESCRIPTION

Rcount is a software for simple and flexible RNA-Seq read counting. Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA- coding genes) or to add flanking regions.

::DEVELOPER

Ueli Grossniklaus’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

 Rcount

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 15. pii: btu680.
Rcount: simple and flexible RNA-Seq read counting.
Schmid MW, Grossniklaus U

Velvet-SC 0.7.62 – Velvet modified for Single Cell reads

Velvet-SC 0.7.62

:: DESCRIPTION

Velvet-SC is a Velvet modified software for Single Cell reads

::DEVELOPER

UCSD Department of Computer Science and Engineering

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  Velvet-SC

:: MORE INFORMATION

Citation

Hamidreza Chitsaz, Joyclyn L. Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo, Christopher L. Dupont, Jonathan H. Badger, Mark Novotny, Douglas B. Rusch, Louise J. Fraser, Niall A. Gormley, Ole Schulz-Trieglaff, Geoffrey P. Smith, Dirk J. Evers, Pavel A. Pevzner, Roger S. Lasken.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.
Nature Biotechnology, vol. 29, no. 11, pp. 915-921 (2011), advance online publication, 18 Sep 2011

Uniprot DAT File Parser 1.1.5674 – Read Uniprot (IPI) .Dat file and Parse out the information for each entry

Uniprot DAT File Parser 1.1.5674

:: DESCRIPTION

The Uniprot DAT File Parser can read a Uniprot (IPI) .Dat file and parse out the information for each entry, creating a tab delimited text file. Uniprot .Dat files can be obtained from EBI’s FTP site.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 3.5

:: DOWNLOAD

 Uniprot DAT File Parser

:: MORE INFORMATION

NoDe – Error-correcting Algorithm for 454 Pyrosequencing Reads

NoDe

:: DESCRIPTION

NoDe (Noise Detector) is a new error correction algorithm which was trained to identify those positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in error-free representative read.

::DEVELOPER

The Bioinformatics team of the Microbiology Unit, SCK.CEN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NoDe

:: MORE INFORMATION

Citation:

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.
Mysara M, Leys N, Raes J, Monsieurs P.
BMC Bioinformatics. 2015 Mar 15;16(1):88.

drFAST 1.0 – di-base Read Fast Alignment Search Tool

drFAST 1.0

:: DESCRIPTION

drFAST is designed to map di-base reads (SOLiD color space reads) to reference genome assemblies; in a fast and memory-efficient manner.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 drFAST

:: MORE INFORMATION

Citation

mrsFAST:

mrFAST:

SAMBLASTER 0.1.26 – Duplicate Marking and Structural Variant Read Extraction

SAMBLASTER 0.1.26

:: DESCRIPTION

samblaster is a tool to mark duplicates and extract discordant and split reads from sam files.

::DEVELOPER

Greg Faust (gf4ea@virginia.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAMBLASTER 

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 7. [Epub ahead of print]
SAMBLASTER: fast duplicate marking and structural variant read extraction.
Faust GG1, Hall IM.

Phusion 2.1c – Assembly Genome Sequences from Whole Genome Shotgun(WGS) Reads

Phusion 2.1c

:: DESCRIPTION

Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads.

::DEVELOPER

Phusion team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Phusion

:: MORE INFORMATION

Citation

The phusion assembler.
Mullikin JC and Ning Z
Genome research2003;13;1;81-90

BCALM 2.2.3 – de Bruijn Graph Compacation from Reads

BCALM 2.2.3

:: DESCRIPTION

BCALM is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BCALM

:: MORE INFORMATION

Citation:

Rayan Chikhi, Antoine Limasset and Paul Medvedev,
Compacting de Bruijn graphs from sequencing data quickly and in low memory,
Bioinformatics, 32 (12), i201-i208 2016 Jun 15