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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 citations

 (21)
library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] base 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 [], which […]

library_books

Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants

2018
BMC Genomics
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 = 81) […]

library_books

Rewired RNAi mediated genome surveillance in house dust mites

2018
PLoS Genet
PMCID: 5805368
PMID: 29377900
DOI: 10.1371/journal.pgen.1007183

[…] Bio 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 sequenc […]

library_books

Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards

2018
Genome Biol Evol
PMCID: 5798147
PMID: 29360978
DOI: 10.1093/gbe/evy013

[…] nd 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 an […]

library_books

Mining of the Uncharacterized Cytochrome P450 Genes Involved in Alkaloid Biosynthesis in California Poppy Using a Draft Genome Sequence

2017
PMCID: 5913652
PMID: 29301019
DOI: 10.1093/pcp/pcx210

[…] imes, 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 M […]

library_books

The complete chloroplast genome sequence of Asian Palmyra palm (Borassus flabellifer)

2017
BMC Res Notes
PMCID: 5732391
PMID: 29246263
DOI: 10.1186/s13104-017-3077-8

[…] ow size of 4 with an average of Phred score ≥ 20 and removal of 5′ and 3′ ends with Phred score ≤ 3 were used as the trimming criteria. By mapping to the cp genome of C. nucifera (NC_022417) [] using SOAPec v2.03, the reads provided an average of 100× sequencing depth coverage, and eight contigs covering 92% of the entire cp genome was obtained. Specific PCR amplification and sequencing were perfo […]


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