NovoAlign pipeline

NovoAlign specifications

Information


Unique identifier OMICS_15074
Name NovoAlign
Software type Package/Module
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS
Computer skills Medium
Version 3.06.05
Stability Stable
Maintained Yes

Subtool


  • NovoBarCode

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Maintainer


  • person_outline NovoSort Team <>

NovoAlign IN pipelines

 (27)
2018
PMCID: 5789682
PMID: 29378665
DOI: 10.1186/s13293-018-0167-9

[…] the ucla clinical genomics center., the sequence reads, fastq files, were aligned to the human reference genome (grch37/hg19 feb. 2009 assembly) using bwa (burrows-wheeler alignment tool) [27] and novoalign (novocraft.com). the output bam files were sorted and merged, and pcr duplicates were removed using picard. indel (insertion and deletion) realignment and recalibration was performed using […]

2018
PMCID: 5804028
PMID: 29391400
DOI: 10.1038/s41398-017-0088-0

[…] sequencers (life technologies, carlsbad, ca, usa). mean depth and coverage rate of all samples are summarized in supplementary table 3., fastq format files were generated by bcl2fastq software. novoalign software (novocraft technologies, kuala lumpur, malaysia) was used to align reads on the hg19/grch37 human reference genome sequence. aligned reads were sorted by novosort software […]

2017
PMCID: 5404241
PMID: 28487704
DOI: 10.3389/fpls.2017.00542

[…] were removed by the software cutadapt (https://github.com/marcelm/cutadapt/) and poly(a)-tails were clipped by an in-house python-script. the reads were aligned to reference sequences using novoalign (http://www.novocraft.com). this tool maps reads to reference sequences depending on certain parameters (i.e., quality) and calculates thresholds for each assignment. the reference […]

2017
PMCID: 5418855
PMID: 28472924
DOI: 10.1186/s12864-017-3741-3

[…] accession numbers are given in additional file 1., next, the reads from each of the six samples were aligned to a set of mirnas that consisted of all known salmo salar mature mirnas [25, 26] using novoalign (http://www.novocraft.com/products/novoalign/). custom made scripts were used to report number of successfully assigned reads to each mirna. the reads mapping with edit distance 1 or less […]

2017
PMCID: 5529667
PMID: 28765789
DOI: 10.1038/hgv.2017.32

[…] libraries were sequenced with hiseq2500 (illumina, ca, usa)., fastq format files were generated by the bcl2fastq software for hiseq2500 and by the miseq reporter software for miseq (illumina). the novoalign software (novocraft, selangor, malaysia) was used to align reads on the hg19/grch37 human reference genome sequence. aligned reads were sorted by the novosort software (novocraft) […]

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