SOAPec protocols

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SOAPec specifications

Information


Unique identifier OMICS_05197
Name SOAPec
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Version 2.01
Stability Stable
Maintained Yes

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SOAPec in pipelines

 (4)
2018
PMCID: 5805368
PMID: 29377900
DOI: 10.1371/journal.pgen.1007183

[…] contigs: a) using trimmomatic [], from both ends of reads, nucleotides with base quality lower than 15 were removed. b) using fastuniq [], duplicate pairs were removed from the pe library, and c) soapec [] was used to correct read error [, ]. any initial genome sequence has bacterial contamination due, at least, to the presence of gut microbiota in dna isolates. to remove bacterial dna […]

2017
PMCID: 5726476
PMID: 29099922
DOI: 10.1093/gigascience/gix102

[…] (). to improve the read quality, we trimmed low-quality bases from both sides of the reads and removed reads with more than 5% of uncalled (“n”) bases. then reads of all libraries were corrected by soapec (version 2.03) []. finally, clean reads amounting to 615 gb were obtained for genome assembly., the estimated genome size is 2.76 gb according to k-mer analysis, based on the following […]

2016
PMCID: 5266360
PMID: 28095660
DOI: 10.3347/kjp.2016.54.6.751

[…] of already old ones. therefore, we continued the study and obtained distinct results in our draft genome of t. canis. in this study, we used more recent versions or new tools as follows: jellyfish, soapec, and gatk for sequencing; repeatrunner, maker, pasa, and blast2go for structural annotation. these results may be able to provide insights into the taxonomy of t. canis, host-parasite […]

2016
PMCID: 5266360
PMID: 28095660
DOI: 10.3347/kjp.2016.54.6.751

[…] system, and performed a k-mer frequency analysis to filter out reads with lower k-mer frequency, which could result from a sequencing error. for all of the read data, an error correction tool, soapec (version 2.01) [], was used for read trimming and base correction, with the k-mer size set to 17. next, gatk [] was used to remove duplicate read pairs, and only 1 read pair […]


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SOAPec in publications

 (26)
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] sliding window having an average phred score of at least 15, and with a minimum sequence length of 70. we corrected possible sequencing errors based on the distribution of kmer frequencies using soapec v2.01 with default settings []. we then built de novo assemblies from the edited reads using soapdenovo2 v2.04 [] and abyss v1.9.0 []. we also assembled the genome with masurca v2.3.2 [], […]

PMCID: 5800051
PMID: 29402214
DOI: 10.1186/s12864-018-4490-7

[…] ive human, fungal and bacterial contamination reads were discarded (deconseq v0.4.2 []). read pairs were synchronized using an in-house script. read error correction was applied on cleaned data using soapec v2.01 (http://soap.genomics.org.cn/). cleaned overlapping miseq reads were merged using flash v1.2.6 []., de novo assembly and scaffolding was performed with abyss v1.3.5 (settings n = 3, k = 8 […]

PMCID: 5798147
PMID: 29360978
DOI: 10.1093/gbe/evy013

[…] uagc, respectively. we trimmed raw reads for nucleotide biases, adaptors, and a quality score cutoff of ≥28 with trimmomatic v0.33 (). we corrected errors in the trimmed sequences using the module soapec in soapdenovo2 (). overlapping reads were joined to form single-end reads using flash v1.2.8 (). we compared the outputs of different genome assembly pipelines including abyss versions 1.3.7 […]

PMCID: 5913652
PMID: 29301019
DOI: 10.1093/pcp/pcx210

[…] respectively, producing a coverage value 790 times the genome size (). the sequences were then assembled by platanus 1.2.1.1 () after the removal of adaptor sequences and an error correction by soapec v2.01 using a k-mer size of 27, a low-frequency k-mer cut-off of 19 and manual correction methods. the sequences were ultimately assembled into 53,253 scaffolds that covered approximately 489 […]

PMCID: 5824821
PMID: 29267854
DOI: 10.1093/gigascience/gix130

[…] (6) duplicated polymerase chain reaction (pcr) sequences. the low-quality bases at heads or tails of reads were also trimmed. after that, the short-insert library reads were corrected using soapec [], a k-mer-based error correction package. this resulted in a 244.84-gb qualified dataset, representing about 82-fold genome coverage (table s1)., the milu genome size (g) was estimated […]


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