<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38041?offset=550 https://bioinformaticsonline.com/bookmarks/view/28999/redundans Thu, 01 Sep 2016 08:28:11 -0500 https://bioinformaticsonline.com/bookmarks/view/28999/redundans <![CDATA[Redundans]]> Redundans pipeline assists an assembly of heterozygous genomes.
Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should be less fragmented and with total size smaller than the input contigs. In addition, Redundans will automatically close the gaps resulting from genome assembly or scaffolding more details.

The pipeline consists of three steps/modules:

  • redundancy reduction: detection and selectively removal of redundant contigs from an initial de novo assembly
  • scaffolding: joining of genome fragments using paired-end and/or mate-pairs reads
  • gap closing

Redundans is:

  • fast & lightweight, multi-core support and memory-optimised, so it can be run even on the laptop for small-to-medium size genomes
  • flexible toward many sequencing technologies (Illumina, 454 or Sanger) and library types (paired-end, mate pairs, fosmids)
  • modular: every step can be ommited or replaced by another tools

Address of the bookmark: https://github.com/Gabaldonlab/redundans

]]> Jit https://bioinformaticsonline.com/file/view/29108/assembly-tutorial-ppt Wed, 07 Sep 2016 03:12:53 -0500 https://bioinformaticsonline.com/file/view/29108/assembly-tutorial-ppt <![CDATA[Assembly tutorial PPT]]> Saved Cornell University assembly workshop PPT.

Reference: 

http://cbsu.tc.cornell.edu/lab/doc/assembly_workshop_20150420_lecture1.pdf

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29142/opera-optimal-paired-end-read-assembler Fri, 09 Sep 2016 05:28:58 -0500 https://bioinformaticsonline.com/bookmarks/view/29142/opera-optimal-paired-end-read-assembler <![CDATA[OPERA : Optimal Paired-End Read Assembler]]> OPERA (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly). It uses information from paired-end/mate-pair/long reads to order and orient the intermediate contigs/scaffolds assembled in a genome assembly project, in a process known as Scaffolding. OPERA is based on an exact algorithm that is guaranteed to minimize the discordance of scaffolds with the information provided by the paired-end/mate-pair/long reads (for further details see Gao et al, 2011).

Note that since the original publication, we have made significant changes to OPERA (v1.0 onwards) including refinements to its basic algorithm (to reduce local errors, improve efficiency etc.) and incorporated features that are important for scaffolding large genomes (multi-library support, better repeat-handling etc.), in addition to other scalability and usability improvements (bam and gzip support, smaller memory footprint). We therefore encourage you to download and use our latest version: OPERA-LG. In our benchmarks, it has significantly improved corrected N50 and reduced the number of scaffolding errors. Furthermore, our latest release contains the wrapper script OPERA-long-read that enables scaffolding with long-reads from third-generation sequencing technologies (PacBio or Oxford Nanopore). The manuscript describing the new features and algorithms is available at Genome Biology. We look forward to getting your feedback to improve it further.

Address of the bookmark: https://sourceforge.net/p/operasf/wiki/The%20OPERA%20wiki/

]]> Jit