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标题： Fast and accurate de novo genome assembly from long uncorrected reads 摘要： The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction step can be omitted and high quality consensus sequences […] NGS数据分析中的质量控制工具，老规矩，先占坑！ 基本介绍 NGS QC-Chain (Zhou et al. 2013)1 http://www.computationalbioenergy.org/qc-chain.html RNA-SeQC (DeLuca et al. 2012)2 https://confluence.broadinstitute.org/display/CGATools/RNA-SeQC HTQC (Yang et al. 2013)3 http://sourceforge.net/projects/htqc/ Trimmomatic (Lohse et al. 2012)4 http://www.usadellab.org/cms/?page=trimmomatic NGS QC Toolkit (Patel and Jain 2012)5 http://www.nipgr.res.in/ngsqctoolkit.html FastUniq (Xu et al. 2012)6 http://sourceforge.net/projects/fastuniq/ RseQC (Wang et al. 2012)7 http://code.google.com/p/rseqc/ CHANCE (Diaz et al. 2012)8 https://github.com/songlab/chance htSeqTools (Planet […] 先在这里开个头，后面不断对这个Topic 进行更新。 基本介绍 K-mer 在生物信息学中有着广泛的应用，比如基因组拼装，评估基因组测序覆盖度，测序数据的纠错，多序列比对，重复序列检测。但是计算K-mer 比较耗费内存，因此好的数据结构有利于降低内存的使用，比如Khmer，采用概率型数据结构（Bloom_filter, http://en.wikipedia.org/wiki/Bloom_filter），Jellyfish 采用了并行无锁哈希表（lock-free hash table）数据结构，为了降低内存使用，有时候可能需要在时间，内存，磁盘空间使用上进行折中。 下面列出了现在比较常用的K-mer计算的工具以及一些应用实例。 工具 DSK (Rizk et al. 2013)1 http://minia.genouest.org/dsk/ Musket (Liu et al. 2013)2 http://musket.sourceforge.net/homepage.htm#latest Khmer (McDonald and Brown 2013)3 http://khmer.readthedocs.org/en/latest/ BFCounter (Melsted and Pritchard 2011)4 http://pritch.bsd.uchicago.edu/bfcounter.html Simrank (DeSantis et al. 2011)5 http://search.cpan.org/~shuriko/String-Simrank-0.079/lib/String/Simrank.pm Kmer (Walenz and Florea 2011)6 http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page Jellyfish (Marcais and Kingsford 2011)7 http://www.cbcb.umd.edu/software/jellyfish/ Tallymer […] Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds links: doi:10.1038/nature12309 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12309.html Genome Sequence and assembly The assembly of E. guineensis (AVROS, pisifera fruit form) genome P5-build was constructed from sequences from a total of 148 linker libraries and 81 fragment libraries (Roche/454). Reads were generated from genomic DNA fragment […] Coelacanth genomes reveal signatures for evolutionary transition from water to land links: http://genome.cshlp.org/content/early/2013/07/19/gr.158105.113.abstract Assembling the coelacanth genome First, we constructed the reference coelacanth draft genome from one of the Tanzanian specimens (TCC041-004, gender unknown; Nikaido et al. 2011), which was recovered from the body cavity of its mother (coelacanths give birth to fully formed offspring; […] Illumina Announces Moleculo Long Read Technology and Phasing As Service links: http://nextgenseek.com/2013/07/illumina-announces-moleculo-long-read-technology-and-phasing-as-service/ Illumina kept its promise of making Moleculo’s Long Read Technoogy as service in 2013. Illumina announced today that Illumina’s FastTrack Services will be offering Long-Read Sequencing Services and new Phasing Analysis. With the two new additional services, Illumina can provide whole-genome results within […] The Norway spruce genome sequence and conifer genome evolution 文章地址： Nature http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12211.html Supplementary Material Haploid whole genome shotgun sequencing and assembly Seeds from the P. abies clone Z4006 were stored at -20° C at Skogforsk Sävar, then soaked in water overnight, and manually dissected under a microscope to free the haploid megagametophyte tissue. Total DNA […] |
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