NextGenMap pipeline

NextGenMap specifications


Unique identifier OMICS_00672
Name NextGenMap
Alternative name Next-Gen Mapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ, SAM, BAM
Output format BAM, SAM
Operating system Unix/Linux, Mac OS, Windows
Parallelization CUDA
Computer skills Advanced
Version 0.5.0
Stability Stable
Source code URL
Maintained Yes



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Publication for NextGenMap

NextGenMap IN pipelines

PMCID: 5510586
PMID: 28717593
DOI: 10.7717/peerj.3529

[…] libraries of the selected projects by (1) quality trimming of all reads with cutadapt version 1.1.3 (martin, 2011; options: -q 25,25 –minimum-length 50 –pair-filter=both) (2) mapping the reads with nextgenmap (min. identity 99%); (3) counting the reads with samtools; (4) normalizing read counts to reads per kilobase per million mapped reads (rpkm) and log 2 transforming this value, (5) […]

PMCID: 4608838
PMID: 26473952
DOI: 10.1371/journal.ppat.1005218

[…] three biological replicates for the cac2δ/δ as well as the rtt109δ/δ mutants were sequenced., reads were mapped onto the assembly 21 of the c. albicans genome ( using nextgenmap [111]. read counts were determined with htseq using the union mode [112] and a reference annotation (c_albicans_sc5314_version_a21-s02-m07-r10; […]

NextGenMap institution(s)
Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria; Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
NextGenMap funding source(s)
This work was supported by Deutsche Forschungsgemeinschaft SPP1174 [HA1628-9-2].

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