Posts Tagged ‘assembly’

TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. – PubMed – NCBI

Sunday, February 21st, 2016

TIGRA: Targeted Iterative Graph Routing Assembler for breakpoint[s ] key steps: read extraction & de Bruijn #assembly

This presents a breakpoint assembler used for many projects including 1000 Genomes. It uses a targeted iterative graph routing approach. The program consists of two steps: read extraction and then assembly. The assembly step uses a de Bruin graph-based approach to create contigs from the selected reads. A shortcoming of TIGRA is it depends on the success of the first step of the program, selection of reads that span breakpoints. Thus TIGRA is sensitive to the breakpoint annotation accuracy input. Breakpoints determined from discordant paired-end or split-end alignments and by predictors like breakdancer, delly, genomestrip are excellent for TIGRA, but those determined only by read-depth such as CNVnator and RDX are poor performers.

As input TIGRA requires putative breakpoints annotation/prediction (preferably at nucleotide level or at least within 100bp resolution) and BAM files (sequence reads aligned to reference genome).
In the read extraction TIGRA tries to select all the reads that are likely associated with the breakpoint as long ass they have at least one ned or subsegment that is confidently mapped. For known SV types, TIGRA extract reads selectively to reduce the over representation of the reference allele. The assembly step uses the a de Bruin graph-based approach to create contigs from the selected reads. For this TIGRA first uses an iterative procedure to explore multiple k-mers and thus increases the chance of assembling of low coverage reads. Next it records alternative path in the contain graph

The landscape of long noncoding RNAs in the human transcriptome : Nature Genetics : Nature Publishing Group

Wednesday, January 28th, 2015

Landscape of lncRNAs in the human #transcriptome Derived from RNAseq read assembly; not much overlap w/ @GencodeGenes

Matthew K Iyer,
Yashar S Niknafs,
Rohit Malik,
Udit Singhal,
Anirban Sahu,
Yasuyuki Hosono,
Terrence R Barrette,
John R Prensner,
Joseph R Evans,
Shuang Zhao,
Anton Poliakov,
Xuhong Cao,
Saravana M Dhanasekaran,
Yi-Mi Wu,
Dan R Robinson,
David G Beer,
Felix Y Feng,
Hariharan K Iyer
& Arul M Chinnaiyan

Nature Genetics (2015) doi:10.1038/ng.3192Received 20 June 2014 Accepted 18 December 2014


Tuesday, November 19th, 2013

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

HaploSeq: #haplotype reconstruction using proximity-ligation. Nice adaptation of functional genomics tech to assembly