NextGenMap protocols

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NextGenMap specifications

Information


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 https://codeload.github.com/Cibiv/NextGenMap/zip/master
Maintained Yes

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Publication for NextGenMap

NextGenMap in pipelines

 (11)
2018
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] trimmed of adapters and low-quality bases, and screened for common contaminants using bbduk2 (bbmap v35.69, http://sourceforge.net/projects/bbmap/). the pool-seq data were mapped to the genome using next-gen mapper v0.4.10 with an identity cutoff of 90% to minimise mapping bias. samtools v1.2 was used to filter the mapped data for only correctly mapped paired-ends reads, after which a mpileup […]

2017
PMCID: 5510586
PMID: 28717593
DOI: 10.7717/peerj.3529

[…] for all libraries of the selected projects by (1) quality trimming of all reads with cutadapt version 1.1.3 (; 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) […]

2017
PMCID: 5510586
PMID: 28717593
DOI: 10.7717/peerj.3529

[…] we downloaded all short read libraries associated with these projects (993 in total, ) and mapped all reads of each of the libraries to the ‘symbionts & pathogens’ reference database using nextgenmap version 0.4.12 (). if at least 1,000 reads of a library were aligned to one or more sequence baits, we extracted the matching reads and assembled them using spades version 3.7 (). contigs […]

2017
PMCID: 5578184
PMID: 28820494
DOI: 10.3390/ijms18081796

[…] 65 bp long reads following the manufacturer’s instructions with an average sequencing depth of 60 million paired-reads. reads were mapped against the human reference genome assembly grch38.80 using nextgenmap (v. 0.4.12, http://cibiv.github.io/nextgenmap/) with default settings []. downstream quantification of genes in raw read counts as well as in rpkm (=reads per kilobase of exon model per […]

2017
PMCID: 5585943
PMID: 28874114
DOI: 10.1186/s12864-017-4097-4

[…] 35 and 12 million reads for neutrophils and for candida transcriptome, respectively., reads were mapped against the human reference genome [hg19] and c. albicans reference genome assembly 21 using nextgenmap (v. 0.4.12) with default settings []. a summary of all analyzed samples for rna-seq including sequencing depth and mapping statistics is listed in additional file : table st1. downstream […]


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NextGenMap in publications

 (41)
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] and sequence files were manipulated using ngs-utils v0.5.7 []. for between population variants, trimmed reads were mapped to the t. orientalis shintoku reference sequence [15] with nextgenmap v0.4.12 []. low quality mapped reads (q < 10) were filtered using samtools v1.2 [] and alignments were subsequently sorted, and duplicates removed using picard tools v1.138 […]

PMCID: 5912717
PMID: 29684023
DOI: 10.1371/journal.pbio.2005129

[…] adapter read-throughs were removed from the raw illumina reads, umis were extracted and stored separately, and the reads (lacking umis) were mapped to the u. maydis reference genome [] using nextgenmap []. the reads mapping to each flank (5' and 3') of each insertional mutant were grouped by umi, and highly similar umis were merged to correct for sequencing errors []. umis with fewer […]

PMCID: 5940141
PMID: 29523635
DOI: 10.1534/g3.117.300394

[…] the datasets generated during the current study are available in the ncbi sequence read archive (https://www.ncbi.nlm.nih.gov/sra)., the reads were mapped against human genome reference (hg19) using nextgenmap () (v0.5.0) with default parameters plus several additional options: identity (-i) was set to 0.85, maximum number of consecutive indels allowed (-c) was set to 120 and we used alignment […]

PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] estimation approaches, and (c) with an additional fold change 2 threshold for significant differential expression. in addition to the mapping approach described above, we used the mapping programs nextgenmap v0.5.0 and rsem v1.2.19. the latter program (which uses bowtie2 internally) was tested using both the unfiltered trinity transcriptome assembly (at both isoform and gene level) […]

PMCID: 5944698
PMID: 29419698
DOI: 10.1097/MD.0000000000009868

[…] to pass the quality filter, read quality needs to surpass a phred score of 20 and achieve a minimal length of 50 bp after trimming of low quality and adapter bases. subsequently, nextgenmap is used to align quality-controlled reads to the human reference genome (hg19) requiring a minimum identity between read and reference genome of 80%. reads mapping to the human reference […]


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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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