Tag: Short Read Mapping

CloudBurst 1.1.0 – Highly Sensitive Short Read Mapping with MapReduce

CloudBurst 1.1.0

:: DESCRIPTION

CloudBurst is a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. It is modeled after the short read mapping program RMAP, and reports either all alignments or the unambiguous best alignment for each read with any number of mismatches or differences. This level of sensitivity could be prohibitively time consuming, but CloudBurst uses the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes.

::DEVELOPER

the Schatz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

CloudBurst

:: MORE INFORMATION

Citation

CloudBurst: Highly Sensitive Short Read Mapping with MapReduce
Michael Schatz
Center for Bioinformatics and Computational Biology, University of Maryland
Bioinformatics 2009 25(11):1363-1369

segemehl 0.3 – Fast Short Read Mapping with Indels

segemehl 0.3

:: DESCRIPTION

segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly.  segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gzip‘ed queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

::DEVELOPER

the Hoffmann Junior Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  segemehl

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 13. [Epub ahead of print]
Lacking alignments? The next generation sequencing mapper segemehl revisited.
Otto C1, Stadler PF, Hoffmann S.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J:
“Fast mapping of short sequences with mismatches, insertions and deletions using index structures“,
PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502

SNP-o-matic 1.0 – Stringent Short-read Mapping software

SNP-o-matic 1.0

:: DESCRIPTION

SNP-O-MATIC is software to analyse Solexa reads and compare them to a reference. The core application, findknownsnps, looks at perfect matches of single and paired Solexa reads to a given reference sequence.

::DEVELOPER

SNP-o-matic team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  SNP-o-matic

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Sep 15;25(18):2434-5. doi: 10.1093/bioinformatics/btp403. Epub 2009 Jul 2.
SNP-o-matic.
Manske HM, Kwiatkowski DP.

DistMap 1.0 – A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

DistMap 1.0

:: DESCRIPTION

DistMap is a user-friendly pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • Perl
  • Mapper executable
  •  MergeSamFiles.jar and SortSam.jar from PICARD (http://picard.sourceforge.net).
  • A working Hadoop cluster.

:: DOWNLOAD

 DistMap

:: MORE INFORMATION

Citation:

Pandey RV, Schlötterer C. (2013)
DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.
PLoS One. 8(8):e72614.

RMAP 2.1 – Short-read Mapping

RMAP 2.1

:: DESCRIPTION

RMAP is aimed to map accurately reads from the next-generation sequencing technology. RMAP can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.

::DEVELOPER

The Smith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RMAP

:: MORE INFORMATION

Citation:

Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z and Zhang MQ (2009)
Updates to the RMAP short-read mapping software.
Bioinformatics 25(21):2841-2842.