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Protocols

RazerS specifications

Information


Unique identifier OMICS_00679
Name RazerS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline David Weese

Publications for RazerS

RazerS citations

 (15)
library_books

Fast and efficient short read mapping based on a succinct hash index

2018
BMC Bioinformatics
PMCID: 5845352
PMID: 29523083
DOI: 10.1186/s12859-018-2094-5

[…] s. The first step of most associated pipelines is the mapping of the generated reads to a reference genome.Read mappers fall into one of the two classes. One class, including FastHASH [], mrsFAST [], RazerS3 [], BitMapper [], and Hobbes [], is referred to as all-mappers. All-mappers attempt to find all mapping locations of each read. The other class, including Bowtie2 [], BWA [], and GEM [], is re […]

library_books

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges

2017
Comput Struct Biotechnol J
PMCID: 5581845
PMID: 28883909
DOI: 10.1016/j.csbj.2017.07.004

[…] o filter clearly false mappings before verification. mrFAST does not support multi-threading, which means it will take a long mapping time when dataset is large.As for coarse-grained parallelization, RazerS3  has developed a load balancing scheme. RazerS3 has implemented a pigeonhole filter, which means it takes much less time to filter less false locations. Since time spent for verification domin […]

library_books

Kart: a divide and conquer algorithm for NGS read alignment

2017
Bioinformatics
PMCID: 5860120
PMID: 28379292
DOI: 10.1093/bioinformatics/btx189

[…] ccept the format of test data (such as Gassst, Ssaha2 and NovoAlign), plus those which could not be run properly in our system or took much more time to process the test data (such as GEM, hobbes and razers3).The selected aligners represent state-of-the-art NGS short read mappers and are widely used in NGS data analysis. We tried to use the default parameter settings to test each aligner unless th […]

library_books

Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

2016
Genome Biol
PMCID: 5114739
PMID: 27855702
DOI: 10.1186/s13059-016-1092-z

[…] ga/studies/EGAS00001000509). BAM files containing whole-exome sequences from normal and/or tumor samples were processed to obtain fastq files. Reads that aligned to HLA-A, HLA-B, or HLA-C genes using RazerS3 [] (http://www.seqan.de/projects/razers/) were passed as input to OptiType v1.0 [] (https://github.com/FRED-2/OptiType). Discrepancies in HLA typing were resolved by consensus or exclusion. A […]

library_books

Classification of different Hepatitis B infected individuals with saturated incidence rate

2016
Springerplus
PMCID: 4947085
PMID: 27468382
DOI: 10.1186/s40064-016-2706-3

[…] ual to another individual on both ways horizontally and vertically, such as transmission of blood, semen, vaginal secretions (Lavanchy ; Lok et al. ; McMahon ), unprotected sexual contact, sharing of razers, blades or tooth brushes (Chang ) and infected mother to her/his child during the time of birth, respectively. However Hepatitis B virus cannot be transmitted through water, food, hugging, kiss […]

call_split

The major horse satellite DNA family is associated with centromere competence

2016
PMCID: 4847189
PMID: 27123044
DOI: 10.1186/s13039-016-0242-z
call_split See protocol

[…] e constituted by the consensus sequences of 37 cen (“SAT_EC” on repbase, [, ]), 2PI (“SAT2pl” on repbase), ERE-1 (“ERE1” on repbase) and EC137 (GenBank JX026961). The alignment was performed with the Razers3 software [] using all of the reads from the paired-end sequencing as a whole single-end dataset; the mapping was carried out using default parameters with exception of percent identity thresho […]

Citations

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RazerS institution(s)
Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
RazerS funding source(s)
Supported by Deutsche Forschungsgemeinschaft [RE-1712/3-1] and the Federal Ministry of Education and Research [16V0080].

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