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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 citations

 (556)
library_books

Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment

2018
Nat Commun
PMCID: 5958119
PMID: 29773874
DOI: 10.1038/s41467-018-04193-w

[…] (51 Mb) Kits (Agilent Technologies). Exome libraries were sequenced on a HiSeq2000 (Illumina) according to the manufacturer’s instructions. Paired reads were aligned to the hg19 human reference using Novoalign V2.08.05 (http://novocraft.com), and single nucleotide variants (SNVs) and insertions and/or deletions (indels) were called using the Genome Analysis Toolkit (GATK) v1.6-13. […]

library_books

Small RNA profiling of low biomass samples: identification and removal of contaminants

2018
BMC Biol
PMCID: 5952572
PMID: 29759067
DOI: 10.1186/s12915-018-0522-7

[…] against the human genome (GRCh37), including RefSeq exon junction sequences, as well as prokaryotic, viral, fungal, plant and animal genomes from GenBank [] and the Human Microbiome Project [] using Novoalign V2.08.02 (Additional file : Tables S3 to S5) []. These organisms were selected based on their presence in the human microbiome, human nutrition and the public availability of the genomes. As […]

library_books

CLIP related methodologies and their application to retrovirology

2018
Retrovirology
PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] The 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 (http://www.novocraft.com/products/novoalign/), RMAP [], TopHat [], GSnap [], SOAP [] and BWA [], some with unique advantages over others depending on whether mapping is done on a genome ver […]

call_split

Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole Genome Phylogenetic Analysis

2018
PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17
call_split See protocol

[…] clonal 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 (Novocraft.com) 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 that were not present […]

library_books

Whole exome sequencing of cell free DNA and circulating tumor cells in multiple myeloma

2018
Nat Commun
PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] ntamination 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 the mutat […]

library_books

Bortezomib prevents cytarabine resistance in MCL, which is characterized by down regulation of dCK and up regulation of SPIB resulting in high NF κB activity

2018
BMC Cancer
PMCID: 5918903
PMID: 29695239
DOI: 10.1186/s12885-018-4346-1

[…] ard/) was used for format conversion and demultiplexing of raw Illumina sequencing data and sequence reads were aligned to the human reference genome hs37d5ss (1000 genome with decoy sequences) using Novoalign (http://www.novocraft.com). Picard MarkDuplicates were used to identify and exclude PCR duplicates in subsequent analyses and quality scores were recalibrated and indels realigned using the […]

Citations

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NovoAlign institution(s)
Novocraft Technologies Sdn Bhd, Petaling Jaya, Selangor, Malaysia

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