SOAPec protocols

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

 (3)
2018
PMCID: 5805368
PMID: 29377900
DOI: 10.1371/journal.pgen.1007183

[…] a) using trimmomatic [63], from both ends of reads, nucleotides with base quality lower than 15 were removed. b) using fastuniq [64], duplicate pairs were removed from the pe library, and c) soapec [65] was used to correct read error [64, 65]. 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

[…]  s1). 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) [4]. 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 formula […]

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) [5], was used for read trimming and base correction, with the k-mer size set to 17. next, gatk [6] was used to remove duplicate read pairs, and only 1 read pair […]

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