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CheckM:微生物基因组组装/metagenome基因组重构完整度和杂合度评估

标题:

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

摘要:

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. While this increasing breadth of draft genomes is providing key information regarding the […]

RNA-seq 序列错误纠正评估

文章:

Optimizing error correction of RNAseq reads

摘要:

Motivation:The correction of sequencing errors contained in Illumina reads derived from genomic DNA is a common pre-processing step in many de novo genome assembly pipelines, and has been shown to improved the quality of resultant assemblies. In contrast, the correction of errors in transcriptome sequence data is […]

Sam/bam 版本 1.5 支持基因组重头数据拼装

文章:

SAM/BAM format v1.5 extensions for de novo assemblies

摘要:

The plain text Sequence Alignment/Map (SAM) file format and its companion binary form (BAM) are a generic alignment format for storing read alignments against reference sequences (and unmapped reads) together with structured meta-data (Li et al., 2009). Driven by the needs of the 1000 Genomes […]

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 […]

Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)

Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)

links: BMC Genomics 2013, 14:490 doi:10.1186/1471-2164-14-490. http://www.biomedcentral.com/1471-2164/14/490/abstract Abstract

Background

Amorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long […]

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; […]

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 […]

NGS++: a library for rapid prototyping of epigenomics software tools

NGS++: a library for rapid prototyping of epigenomics software tools

文章地址:NGS++: a library for rapid prototyping of epigenomics software tools

Abstract Motivation: The development of computational tools to enable testing and analysis of high-throughput–sequencing data is essential to modern genomics research. However, although multiple frameworks have been developed to facilitate access to these tools, comparatively […]

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 […]