NovoSort protocols

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NovoSort specifications

Information


Unique identifier OMICS_15077
Name NovoSort
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Input format BAM
Output format BAM, BAI
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 1.03.05
Stability Stable
Maintained Yes

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  • person_outline NovoSort Team <>

NovoSort in pipelines

 (6)
2018
PMCID: 5804028
PMID: 29391400
DOI: 10.1038/s41398-017-0088-0

[…] 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 (novocraft) and subjected to the marking of pcr and optical duplication by markduplicates in the picard tools package (http://broadinstitute.github.io/picard/). the genome analysis […]

2017
PMCID: 5407242
PMID: 28448065
DOI: 10.1038/sdata.2017.44

[…] reads were mapped to the non-redundant sequence of bac clusters with bwa mem version 0.7.12. the resultant alignment files were converted to bam format with samtools (version 0.1.19), sorted with novosort (novocraft technologies sdn bhd, malaysia, http://www.novocraft.com/) and merged into a single bam files with picard (version 1.128, http://broadinstitute.github.io/picard/). multi-sample […]

2017
PMCID: 5407242
PMID: 28448065
DOI: 10.1038/sdata.2017.44

[…] were mapped as single ends to the non-redundant sequence using bwa mem version 0.7.12 (ref. ) with parameters ‘-m –p –s’ and then converted to bam format with samtools. after duplicate removal with novosort (novocraft technologies sdn bhd, malaysia, http://www.novocraft.com/), bam files were sorted by read name to group the two mates of a pair together. hi-c mapping information […]

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

[…] 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) and were subjected to marking of pcr and optical duplication by markduplicates in the picard tools package (http://broadinstitute.github.io/picard/)., the genome […]

2017
PMCID: 5548758
PMID: 28790370
DOI: 10.1038/s41598-017-06387-6

[…] of 30x. reads were aligned to the hg19 human reference sequence (build grch37) with novoalign (version 3.02.08). the aligned reads were sorted by base pair position and duplicates were marked using novosort. discordant reads were marked with samblaster (version 0.1.20) and sent to a separate file for manual inspection of breakpoints using the igv (version 2.3.61). svs were manually investigated […]


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NovoSort in publications

 (12)
PMCID: 5895680
PMID: 29372282
DOI: 10.1007/s00122-018-3055-0

[…] barley genome sequencing consortium ) using bwa-mem version 0.7.12 (li ). after conversion to bam format with samtools (li et al. ), the resulting alignments were sorted and indexed with novosort (http://www.novocraft.com/products/novosort/). snp calling was performed with samtools version 1.3 (li ) using the commands ‘samtools mpileup –dv’ and ‘bcftools call –c –f gq’. the resulting […]

PMCID: 5748719
PMID: 29261115
DOI: 10.3390/genes8120401

[…] the reference transcriptome and further count reads based on the resulting alignment and provided annotation. resulting alignment files were treated using samtools (version 1.3) [] and sorted with novosort (version 1.2.30) [] as an intermediate step. regardless of the method, estimated read counts were submitted to edger (r version 3.4.0) [] for differential expression analyses, which include […]

PMCID: 5623100
PMID: 29018459
DOI: 10.3389/fpls.2017.01620

[…] version 0.7.15 (li, ) with default parameters. the resulting sam files were converted to bam format with samtools (li et al., ). sorting and detection of optical and pcr duplicates was done with novosort (http://www.novocraft.com/products/novosort/). samtools version 1.3 (li, ) was used for multiple-sample genotype calling at single-nucleotide polymorphism (snp) sites which were previously […]

PMCID: 5508130
PMID: 28691711
DOI: 10.1038/ncomms15999

[…] base qualities of ten and below. after gatk processing, reads were mapped to mm10 using burrows-wheeler aligner version 0.7.7 with the mem algorithm. reads were sorted with novoalign v2.08.03 novosort. pcr/optical duplicates were marked by picard. base-quality recalibration and localized indel realignment was performed using gatk., joint variant calling was performed to identify single […]

PMCID: 5492891
PMID: 28662698
DOI: 10.1186/s12915-017-0387-1

[…] in binary alignment/map (bam) format were merged into a single bam file for each sample using samtools (version 1.3). bam files were then sorted based on chromosome coordinates of alignments using novosort (novocraft version 3.02; rrid: scr_014818). the total number of reads from the mov10 ip was 98,884,367, the number of aligned reads was 71,522,027 (74.59% aligned), and the number […]


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