Pathoscope 2.0.6 / Clinical PathoScope 1.0.4 – Species Identification and Strain Attribution with Unassembled Sequencing data

Pathoscope 2.0.6  / Clinical PathoScope 1.0.4

:: DESCRIPTION

Pathoscope takes a next-generation sequencing reads from a mixture sample of multiple strains of genomes and it predicts which genomes potentially belongs there. Different from most of approach including composition method or similarity search with a daunting task of de novo assembly, the software applies the propagation of evidence in the Bayesian framework to an initial alignment result and reassign an correct membership of mapping by using the expectation and maximization algorithm.

Clinical Pathoscope is a program to identify pathogens/commensals/contaminants in unassembled sequencing reads.

::DEVELOPER

W. Evan Johnson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Pathoscope / Clinical PathoScope

:: MORE INFORMATION

Citation

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.
Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.
Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33.

Genome Res. 2013 Oct;23(10):1721-9. doi: 10.1101/gr.150151.112.
Pathoscope: Species identification and strain attribution with unassembled sequencing data.
Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE.

BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262.
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.
Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA1, Johnson WE.

QCluster – Extending Alignment-free Measures with Quality Values for Reads Clustering

QCluster

:: DESCRIPTION

Qcluster is a software of extending alignment-free measures with quality values for reads clustering.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QCluster

:: MORE INFORMATION

Citation

Clustering of reads with alignment-free measures and quality values.
Comin M, Leoni A, Schimd M.
Algorithms Mol Biol. 2015 Jan 28;10:4. doi: 10.1186/s13015-014-0029-x

absee 1.0 – Reads ABIF files

absee 1.0

:: DESCRIPTION

 absee is a Ruby gem that reads ABIF files (DNA sequencing chromatograms). The software extracts the peak indexes, called sequence, and ACGT values from sequencing files

::DEVELOPER

Jenny Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • Ruby

:: DOWNLOAD

 absee

:: MORE INFORMATION

RAUR – Re-alignment of unmapped Reads with base Quality Score

RAUR

:: DESCRIPTION

RAUR is to re-align the reads that can not be mapped by alignment tools. It takes advantages of the base quality scores (reported by the sequencer) to figure out the longest segment of a read with at most K low quality bases. Combined with an alignment tool (like bwa or bowtie2), RAUR re-align the trimmed reads.

::DEVELOPER

RAUR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Perl

:: DOWNLOAD

 RAUR

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015 Mar 18;16 Suppl 5:S8. doi: 10.1186/1471-2105-16-S5-S8. Epub 2015 Mar 18.
Re-alignment of the unmapped reads with base quality score.
Peng X, Wang J, Zhang Z, Xiao Q, Li M, Pan Y.

harp 20140925 – Haplotype Analysis of Reads in Pools

harp 20140925

:: DESCRIPTION

harp : Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. harp implements an EM algorithm to calculate the frequencies of known haplotypes from pooled sequence data.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 harp

 :: MORE INFORMATION

Citation

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data
Darren Kessner; Tom Turner; John Novembre
Mol Biol Evol (2013) 30 (5): 1145-1158. doi: 10.1093/molbev/mst016

Acacia 1.53 – Error-corrector for Pyrosequenced Amplicon Reads

Acacia 1.53

:: DESCRIPTION

The Acacia program was implemented to correct errors in pyrosequenced amplicons quickly and with high specificity.

::DEVELOPER

CSIRO Bioinformatics

:: SCREENSHOTS

Acacia

:: REQUIREMENTS

  • Linux / Windows / MacOSX
  • Java

:: DOWNLOAD

 Acacia

:: MORE INFORMATION

Citation

Fast, accurate error-correction of amplicon pyrosequences using Acacia.
Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW.
Nat Methods. 2012 Apr 27;9(5):425-6. doi: 10.1038/nmeth.1990.

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.

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.

Btrim – Trim Adapters and Low Quality Regions in Reads

Btrim

:: DESCRIPTION

Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.

::DEVELOPER

Yong Kong yong.kong@yale.edu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 Btrim

:: MORE INFORMATION

Citation

Genomics. 2011 Aug;98(2):152-3. doi: 10.1016/j.ygeno.2011.05.009. Epub 2011 May 30.
Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.
Kong Y.