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AutoSeqMan:batch assembly of contigs for Sanger sequences

Zoological Research 2018年第2期39卷 123-126页

作者： Jie-Qiong Jin Yan-Bo Sun State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences

With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan （in the LaserGene package） is an excellent program with an easy-to-use graphical user interface （GUI） employed to assemble Sanger sequences into contigs. However, with increasing data size, larger sample sets and more sequenced loci make contig assemble complicated due to the considerable number of manual operations required to run SeqMan. Here, we present the ＇autoSeqMan＇ software program, which can automatedly assemble contigs using SeqMan scripting language. There are two main modules available, namely, ＇Classification＇ and ＇assembly＇. Classification first undertakes preprocessing work, whereas assembly generates a SeqMan script to consecutively assemble contigs for the classified files. Through comparison with manual operation, we showed that autoSeqMan saved substantial time in the preprocessing and assembly of Sanger sequences. We hope this tool will be useful for those with large sample sets to analyze, but with little programming experience. It is freely available at https：//***/ Sun-Yanbo/autoSeqMan.

关键词： Batch processing Sanger sequences contig assembly SeqMan

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Genome-wide SNP in silico detection of Lentinula edodes via whole genome sequencing

Genome-wide SNP in silico detection of Lentinula edodes via ...

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中国菌物学会第五届会员代表大会暨2011年学术年会

作者： CHEN Xiang BAO Da-Peng (National Research Center for Edible Fungi Biotechnology and Engineering Key Laboratory of Applied Mycological Resources and Utilization,Ministry of Agriculture,China Shanghai Key Laboratory of Agricultural Genetics and Breeding Institute of Edible Fungi,Shanghai Academy of Agricultural Sciences,Shanghai,China)

＜正＞Analysis of single nucleotide polymorphisms（SNPs） emerges as an important tool in evolutionary biology and *** we report the in silico discovery and analysis of SNPs across the whole genome of two protoplast monokaryons（TPMs） of basidiomycete fungi Lentinula edodes via the high-throughput sequencing *** our knowledge,this is a novel study in which different protoplast monokaryons are utilized for SNPs detection and *** sequence information including 210M and 250M nucleotide bases was generated from TPMs yielding approximately 80%of whole genome *** used surpassed 380K and 410K reads of TPMs for the de novo assembly of two contig sets with an overall estimated depth of 5.67-fold and 6.05-fold coverage,*** of the contigs between TPMs identified 108,235 putative SNPs owning a high probability of at least 10-fold *** SNPs reveal TPMs having similar intra-strain SNP frequencies,and the ratio of transition to transversion among these SNPs being similar to the ratio reported in other *** verify the confidence of detected SNPs,25,044 SNPs were mapped onto 43,912 positions that uniformly distributed over the sequenced chromosomes of Coprinopsis *** result shows high sequence conservation among closely related fungal *** addition,the gene structure of TPMs was constructed for SNPs classification according to their distribution in genome ***,this study indicates the utility of using next generation sequencing technologies to identify large numbers of reliable ***,the method combination of SNP detection and novel algorithm allows an efficient approach for the development of high-density genotyping platforms in fungal species.

关键词： Lentinula edodes whole genome sequencing contig assembly SNPs

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