PgSA 1.2 – Index allowing Queries for a collection of Sequencing Reads

PgSA 1.2

:: DESCRIPTION

PgSA (Pseudogenome Suffix Array) is a compact index for collections of reads from sequencing. It allows to ask for presence of k-mers in the reads.

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PgSA

:: MORE INFORMATION

Citation

PLoS One. 2015 Jul 16;10(7):e0133198. doi: 10.1371/journal.pone.0133198. eCollection 2015.
Indexing Arbitrary-Length k-Mers in Sequencing Reads.
Kowalski T, Grabowski S, Deorowicz S.

MuGI 1.0 – Multiple Genome Index

MuGI 1.0

:: DESCRIPTION

MuGI is a compressed index of collections of genomes of the same species. It allows to ask for both exact and approximate queries. The input data must be given as a reference sequence and Variant Call Format (VCF) file describing the differences between individual genomes and reference genome.

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • C++ Compiler

:: DOWNLOAD

 MuGI

:: MORE INFORMATION

Citation

Indexes of large genome collections on a PC.
Danek A, Deorowicz S, Grabowski S.
PLoS One. 2014 Oct 7;9(10):e109384. doi: 10.1371/journal.pone.0109384.

GSI 0.92 – Genealogical Sorting Index

GSI 0.92

:: DESCRIPTION

The GSI (genealogical sorting index) quantifies the degree of exclusive ancestry of labeled groups on a rooted genealogy

::DEVELOPER

Michael P. Cummings , Maile Neel , Kerry Shaw ,  Adam Bazinet

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GSI

:: MORE INFORMATION

Citation:

Cummings, Neel and Shaw 2008
A genealogical approach to quantifying lineage divergence.
Evolution. 2008 Sep;62(9):2411-22. Epub 2008 Jun 28.

Gk-arrays 2.1.0 – Data Structure to Index the K-mers in a Collection of Reads

Gk-arrays 2.1.0

:: DESCRIPTION

Gk-arrays are provided as a simple-to-use C++ library dedicated to queries on large collection of sequences as produced by high-throughput sequencers (e.g. HiSeq 2000 from Illumina, 454 from Roche).Gk-arrays index k-mers of reads and allow to answer different queries on that read collection.

::DEVELOPER

Gk-arrays team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

 Gk-arrays

:: MORE INFORMATION

Citation

Philippe N., Salson M., Lecroq T., Leonard M., Commes T., Rivals E.
Querying large read collections in main memory: a versatile data structure.
BMC Bioinformatics 2011, 12:242.

GEM library PR3 – Index/Analyze Huge Genomes

GEM library PR3

:: DESCRIPTION

GEM Library  (GEnome Multi-tool)  is a set of very optimized tools for indexing/querying huge genomes/files. Provided so far are a very fast exhaustive mapper (the GEM mapper), an unconstrained split mapper (the GEM split mapper), and a very fast program to compute genome mappability (the GEM mappability).

::DEVELOPER

GEM library Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GEM library

:: MORE INFORMATION

MPscan – Index free Mapping of multiple short reads on a Genome

MPscan

:: DESCRIPTION

The program mpscan (Multi Pattern Scanner) is a software that performs Set Pattern Matching on nucleotitic sequences (DNA/RNA): it searches for a large set of patterns at once in a sequence.

::DEVELOPER

Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 MPscan

:: MORE INFORMATION

Citation

Rivals E., Salmela L., Kiiskinen P., Kalsi P., Tarhio J.
mpscan: Fast Localisation of Multiple Reads in Genomes
Lecture Notes in BioInformatics (LNBI), Springer-Verlag, Vol. 5724, p. 246-260, 2009.

HS – A new index of Host Specificity

HS

:: DESCRIPTION

HS (host specificity) provided here calculates an index of host specificity for parasites based on the number of species, genera, families, orders, and classes in which a species is found. It incorporates the hierarchical information about host distribution included in the Linnean hierarchy, but it is not explcitly tree based.

::DEVELOPER

Kent Holsinger

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

  HS

:: MORE INFORMATION

WinIAP – Ion Activities and Calcite Saturation Index

WinIAP

:: DESCRIPTION

WinIAP calculates the ion activity products and the calcite saturation index for a given set of ions in a solution.

::DEVELOPER

SequentiX

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

WinIAP

:: MORE INFORMATION

This software is free for private and scientific purposes!

RNAsifter 1.0 – RNA Shape Index Filter

RNAsifter 1.0

:: DESCRIPTION

RNAsifter is a non-rigorous filter for the rfam database, that is based on the abstract shape approach. It exploits the familily specific secondary structure, i.e. it computes shapes for the query-sequence and compares them to a precalculated shape-index. The exact matches deliver – hopefully only few – candiate families in which the query-sequence might fold. Membership for the candidate families is checked with the program cmsearch, afterwards.

RNAsifter Online Version

::DEVELOPER

S. Janssen, J. Reeder and R. Giegerich.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • perl

:: DOWNLOAD

RNAsifter

:: MORE INFORMATION

Citation

S. Janssen, J. Reeder and R. Giegerich.
Shape based indexing for faster search of RNA family databases.
BMC Bioinformatics. 2008 Feb 29;9:131.