Archives

IDBA-MT: 元转录组数据拼装工具

标题:

IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology

摘要:

High-throughput next-generation sequencing technology provides a great opportunity for analyzing metatranscriptomic data. However, the reads produced by these technologies are short and an assembling step is required to combine the short reads into longer contigs. As there are many repeat patterns […]

IDBA-UD: 针对单细胞以及元基因组的序列组装软件

标题:

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

摘要:

Motivation: Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from […]

Miniasm+Racon:快速准确完成三代测序数据拼装

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

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 […]

K-mer在生物信息学中的应用及其工具列表

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

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

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

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

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 […]

Insights into the phylogeny and coding potential of microbial dark matter

Insights into the phylogeny and coding potential of microbial dark matter

Supplementary Information

SAG assembly

The draft genome of all but 13 SAGs was generated at the DOE Joint genome Institute (JGI) using the Illumina technology. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform. All general […]