NovoAlign protocols

View NovoAlign computational protocol

NovoAlign statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left Read alignment Reference-assisted assembly chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

NovoAlign specifications


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


  • NovoBarCode



Add your version


  • person_outline NovoSort Team <>

NovoAlign in pipelines

PMCID: 5763532
PMID: 29321003
DOI: 10.1186/s12864-017-4375-1

[…] adapter trimming, error removing and quality control using afterqc [], good quality reads were mapped directly to mirbase (release 21) database of all mature mir sequences using novocraft’s novoalign tool. this allowed us to create raw count tables accounting for every present mir. raw counts were then normalized using standard transcripts per million (tpm) normalization. length of mirs […]

PMCID: 5766599
PMID: 29330370
DOI: 10.1038/s41598-017-18407-6

[…] with total junction flanking transcriptomic sequence summarized from gencode, emsemble and refseq annotations. the junction flanking sequence length was defined by the read length subtract 5. novoalign+ v2.08.01 was used for alignment. redundant mapping at the same locus for both genome and transcriptome was consolidated as one single hit. the read count for each annotated transcript […]

PMCID: 5789682
PMID: 29378665
DOI: 10.1186/s13293-018-0167-9

[…] at 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) [] and novoalign ( 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 […]

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 ., 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 […]

PMCID: 5850229
PMID: 29431102
DOI: 10.1161/JAHA.117.006428

[…] subsequently procured from the unaffected sibling underwent wes utilizing the agilent sureselect human all exon v5+utrs for exome capture. reads were aligned to the hg19 reference genome using novoalign (, followed by sorting and marking of duplicate reads using picard ( local realignment of insertions and deletions and base quality score […]

To access a full list of citations, you will need to upgrade to our premium service.

NovoAlign in publications

PMCID: 5945626
PMID: 29748565
DOI: 10.1038/s41467-018-03917-2

[…] rt-pcr products were mixed and sequenced using the ion torrent pgm and a 318 chip with 850 flows. data were converted to fastq format and aligned to the parp1 cdna sequence (enst00000366794) using novoalign (novocraft technologies). mutations were called from the alignments using the ensembl variant effect predictor rest api (implementation: […]

PMCID: 5946721
PMID: 29719263
DOI: 10.1016/j.celrep.2018.04.004

[…] in . reverse transcription and linearization were performed using rt primer and cut oligo as mentioned in . sequencing for clip was performed on the illumina miseq platform. reads were aligned with novoalign (novocraft technologies), with duplicates collapsed using tools from the cross-induced mutation sites (cims) pipeline and reads per transcript counted with htseq (, ). genome coverage […]

PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] reads that pass the above filtering steps are mapped onto reference genomes or transcriptomes. the most commonly used mapping algorithms used for this task include bowtie [], bowtie2 [], star [], novoalign (, rmap [], tophat [], gsnap [], soap [] and bwa [], some with unique advantages over others depending on whether mapping is done on a genome […]

PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17

[…] complexes () (, )., the bioinformatics pipeline nasp () was used to detect snps among genomes. in brief, reads were aligned to the finished genome fpr3757 (genbank accession no. cp000255) using novoalign ( and snps were called with gatk (). data filtered out included snp loci with less than 5× coverage or less than 80% consensus in any one sample, snp loci […]

PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] levels using contest and filtered out potential artifactual oxog mutations using the oxog3 filter and annotated mutation with oncotater. then, we realigned reads around mutated sites with novoalign to hg19 including decoy sequences and re-ran mutect to filter out mutations in problematic regions. to call somatic insertions and deletions (indels), we used strelka and annotated […]

To access a full list of publications, you will need to upgrade to our premium service.

NovoAlign reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review NovoAlign