SOAPnuke protocols

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SOAPnuke specifications


Unique identifier OMICS_25036
Name SOAPnuke
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.6.2
Stability Stable
boost, zlib, log4cplus, openssl, R
Maintained Yes



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  • person_outline Qiang Chen <>
  • person_outline Lin Fang <>
  • person_outline Yuxin Chen <>
  • person_outline Yongsheng Chen <>
  • person_outline Chunmei Shi <>

Publication for SOAPnuke

SOAPnuke in pipelines

PMCID: 5515834
PMID: 28769960
DOI: 10.3389/fpls.2017.01257

[…] using the nebnext® ultratm rna library prep kit for illumina® (neb, united states). then, the library was sequenced using an illumina hiseq 4000, and 150-bp paired-end reads were generated., soapnuke software was used to filter reads. primary sequencing data (called raw reads) were cleaned by removing reads with adapters. a low-quality read was defined based on the percentage of bases […]

PMCID: 5547133
PMID: 28785026
DOI: 10.1038/s41598-017-06828-2

[…] region. all the enriched libraries were paired-end sequenced using illumina hiseq. 2500 (illumina, san diego, ca, usa) with a read length of 101 bp., the low quality reads were removed using soapnuke software parameter -l 10 -q 0.5 -n 0.1. the bwa software (0.7.12) was used to align reads to the human reference genome (hg19, grch37). the variants in the genomic dna samples […]

PMCID: 5731807
PMID: 28837390
DOI: 10.1080/15476286.2017.1367890

[…] were cleaned by filtering out adaptor sequences, low-quality reads with unknown bases (n bases) >10%, and sequences whose proportion of low-quality bases (q value ≤ 10) was more than 50% using soapnuke software ( clean paired-end reads were mapped to the b. belcheri genome (v18h27.r3) using tophat, allowing no more than five mismatches per read […]

PMCID: 5919727
PMID: 29242387
DOI: 10.1534/g3.117.300495

[…] paired-end, genotyping-by-sequencing (gbs) libraries were prepared with the 5-bp cutter apeki, pooled, and sequenced on a single lane of illumina 4000 ()., bgi filtered the raw data through their soapnuke filter, which includes demultiplexing the reads, removing proprietary barcode sequences, and dropping reads that were >26% adapter sequence and/or where >40% of the bases […]

PMCID: 5005354
PMID: 27630619
DOI: 10.3389/fmicb.2016.01346

[…] basecaller (v1.9.4) combines these per-cycle bcl files from a run and translates them into qseq files. raw reads were trimmed of adaptor sequences, sequencing primers, and multiplex barcode using soapnuke software (bgi), and clean reads of 90 bp were obtained by filtering out low quality reads including those with unknown nucleotides larger than 5%, reads with more than 50% of the bases' […]

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SOAPnuke in publications

PMCID: 5941690
PMID: 29739312
DOI: 10.1186/s12864-018-4747-1

[…] finally, sequencing of the libraries was performed using illumina hiseq 2000 at the beijing genomics institute (shenzhen, china)., the raw reads were subjected to quality control through soapnuke tool, and low quality reads, including reads with adapters, reads in which unknown bases were more than 10%, and reads in which the percentage of the low quality bases (quality value ≤10) […]

PMCID: 5920169
PMID: 29700164
DOI: 10.1128/genomeA.00362-18

[…] these underwent 2 × 150-bp sequencing on a hiseq x ten sequencing platform (illumina, san diego, ca, usa) at the beijing genomics institute (shenzhen, china)., raw reads were preprocessed using soapnuke () and assembled using the a5-miseq pipeline (). contigs were binned and clustered on the basis of tetranucleotide frequency, g+c content, and differential coverage using binsanity (). reads […]

PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] strategy were carried out at bgi. illumina reads with adapter contaminations, or with more than 10% of ambiguous bases or with more than 40% of low quality (q score < 20) bases were discarded by soapnuke v.1.5.2 (developed by gbi). the quality of processed reads was checked with fastqc v.0.11.2 ( pacbio polymerase reads […]

PMCID: 5832105
PMID: 29666643
DOI: 10.1155/2018/2439527

[…] truseq rna kit from illumina (san diego, ca) and sequenced on a hiseq 4000 sequencer (bgi hong kong). the reads generated were paired-end and of length 100-nt. raw reads were cleaned up by bgi with soapnuke to remove adapters and low-quality reads. all other command line software tools were installed and used on the high performance computer cluster at university of notre dame center […]

PMCID: 5833690
PMID: 29434213
DOI: 10.1038/s41419-017-0242-x

[…] mrna was enriched with poly-a selection and 50 base pair paired-end rna-seq was completed on bgiseq-500 platform at beijing genomics institute (bgi-shenzhen). raw reads were filtered using soap and soapnuke and clean reads were mapped to transcriptome of refseq database using bowtie2. gene expression was counted by rsem, and normalized as tpm (transcripts per kilobase of exon model per million […]

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SOAPnuke institution(s)
BGI-Shenzhen, Shenzhen, China; Geneplus-Beijing, Beijing, China; Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, China; Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou, China; Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha, China; Intel China Ltd., Shanghai, China; Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China; Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; James D. Watson Institute of Genome Sciences, Hangzhou, China
SOAPnuke funding source(s)
Supported by Collaborative Innovation Center of High Performance Computing, Critical Patented Project of the Science & Technology Bureau of Fujian Province, China (Grant No. 2013YZ0002-2) and the Joint Project of Natural Science and health Foundation of Fujian Province, China (Grant No.2015J01397).

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