Mate-pair文库制备旨在生成一些短的DNA片段,这些片段包含基因组中较大跨度(2-10 kb)片段两端的序列,更具体地说:首先将基因组DNA随机打断到特定大小(2-10 kb范围可选);然后经末端修复,生物素标记和环化等实验步骤后,再把环化后的DNA分子打断成400-600 bp的片段并通过带有链亲和霉素的磁珠把那些带有生物素标记的...
在Illumina科学家Karine Martinez-Viaud和约翰霍普金斯大学Aleksey Zimin的领导下,研究人员利用Illumina测序数据和几种新的文库制备技术,包括10x Genomics的Linked-Reads、mate pairs、long insert配对末端和标准配对末端,来改善宽吻海豚的基因组组装。 他们利用商业化的DeNovoMAGIC™组装软件,产生了两个版本的组装。一个是...
An adapter sequence is incorporated between the junction site of the mate pairs, the length of which is evenly controlled by nick translation. We present a comparison of results from 3 Kb E. coli and Plasmodium falciparum 3D7 mate-pairs made with our protocol, alongside commercial mate-pair ...
De novosequencing usually relies on a hybrid approach for assembling the genome: reads from long-insert paired-end sequencing, referred to asmate-pair sequencing(with higher error rate), are used to build a scaffold, and reads f...
Long Mate Pair libraries 接头序列:technote_nextera_matepair_data_processing.pdf 针对此类数据的处理软件主要是:nextclip和skewer,从文章结果来看后者略优。【Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads】 ...
%MappedinPairs: Thepercentageofreadswhosematepairwasalsoalignedtothereference.%Duplication: Thepercentageofmappedsequencethatismarkedasduplicate. %Chimeras: Thepercentageofreadsthatmapoutsideofamaximuminsertsizeorthathavethetwoendsmappingtodifferentchromosomes.ThisdataillustratesthattheNEBNextUltraIIDNALibraryPrepKit...
The default behaviour expects fastq files from a Nextera Mate-Pair library kit in reverse-forward orientation. Output: Based on the location of the Nextera junction adapter (if detected), nxtrim produces four different "virtual libraries": mp: read pairs that are large insert-size mate-pairs,...
% Mapped in Pairs: The percentage of reads whose mate pair was also aligned to the reference. % Duplication: The percentage of mapped sequence that is marked as duplicate. % Chimeras: The percentage of reads that map outside of a maximum insert size or that have the two ends mapping to ...
To do so, it looks for pairs of reads in which the STR-containing read or its mate pair overlap a samples's heterozygous SNP. In these instances, the quality score for the overlapping base can be used to determine the likelihood that the read came from each haplotype. Alternatively, when...
20 Illumina DRAGEN Bio-IT Platform v3.5 User Guide u pe-max-penalty The pe-max-penalty option limits how much the estimated MAPQ for one read can increase because its mate aligned nearby. A paired alignment is never assigned MAPQ higher than the MAPQ that it...