<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37840?offset=520 https://bioinformaticsonline.com/bookmarks/view/34443/opera-an-optimal-genome-scaffolding-program Mon, 27 Nov 2017 10:18:20 -0600 https://bioinformaticsonline.com/bookmarks/view/34443/opera-an-optimal-genome-scaffolding-program <![CDATA[Opera: An optimal genome scaffolding program]]> Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly image). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes.

Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y.

Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

Address of the bookmark: https://sourceforge.net/projects/operasf/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34488/scripts-for-the-analysis-of-hgt-in-genome-sequence-data Wed, 29 Nov 2017 16:44:10 -0600 https://bioinformaticsonline.com/bookmarks/view/34488/scripts-for-the-analysis-of-hgt-in-genome-sequence-data <![CDATA[Scripts for the analysis of HGT in genome sequence data.]]> Scripts for the analysis of HGT in genome sequence data

Address of the bookmark: https://github.com/reubwn/hgt

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34571/mugsy-multiple-whole-genome-alignment-tool Fri, 08 Dec 2017 17:41:14 -0600 https://bioinformaticsonline.com/bookmarks/view/34571/mugsy-multiple-whole-genome-alignment-tool <![CDATA[Mugsy: multiple whole genome alignment tool]]> Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

Address of the bookmark: http://mugsy.sourceforge.net/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34867/magic-blast-a-tool-for-mapping-large-next-generation-rna-or-dna-sequencing-runs-against-a-whole-genome-or-transcriptome Tue, 26 Dec 2017 22:23:39 -0600 https://bioinformaticsonline.com/bookmarks/view/34867/magic-blast-a-tool-for-mapping-large-next-generation-rna-or-dna-sequencing-runs-against-a-whole-genome-or-transcriptome <![CDATA[Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.]]> Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

Address of the bookmark: https://ncbi.github.io/magicblast/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36830/crossmap-a-program-for-convenient-conversion-of-genome-coordinates Thu, 31 May 2018 06:00:47 -0500 https://bioinformaticsonline.com/bookmarks/view/36830/crossmap-a-program-for-convenient-conversion-of-genome-coordinates <![CDATA[CrossMap: a program for convenient conversion of genome coordinates]]> Address of the bookmark: http://crossmap.sourceforge.net

]]> Jit https://bioinformaticsonline.com/file/view/36952/getoptspl-file Fri, 15 Jun 2018 04:43:03 -0500 https://bioinformaticsonline.com/file/view/36952/getoptspl-file <![CDATA[getopts.pl file]]> SSPACE_longread complain for getopts.pl file.

To resolve this, download and have in SSPACED-Longreads folder.

Cheers :)

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38053/swgis-v20-a-seqword-genomic-island-sniffer Thu, 01 Nov 2018 12:35:52 -0500 https://bioinformaticsonline.com/bookmarks/view/38053/swgis-v20-a-seqword-genomic-island-sniffer <![CDATA[swgis v2.0 : a seqword genomic island sniffer]]> swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in the eugi database.

download swgis v2.0

Address of the bookmark: http://eugi.bi.up.ac.za/eugi_download_swgis.php

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/38224/novograph-building-whole-genome-graphs-from-long-read-based-de-novo-assemblies Thu, 15 Nov 2018 12:48:30 -0600 https://bioinformaticsonline.com/bookmarks/view/38224/novograph-building-whole-genome-graphs-from-long-read-based-de-novo-assemblies <![CDATA[NovoGraph: building whole genome graphs from long-read-based de novo assemblies]]> NovoGraph: building whole genome graphs from long-read-based de novo assemblies

An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnically-diverse human genomes.

 

https://f1000research.com/articles/7-1391/v1

Address of the bookmark: https://github.com/NCBI-Hackathons/NovoGraph

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38672/ltr-retriever-accurately-identifies-and-annotates-ltr-retrotransposons-and-use-lai-to-evaluates-the-continuity-of-genome-assemblies Sun, 13 Jan 2019 07:14:31 -0600 https://bioinformaticsonline.com/bookmarks/view/38672/ltr-retriever-accurately-identifies-and-annotates-ltr-retrotransposons-and-use-lai-to-evaluates-the-continuity-of-genome-assemblies <![CDATA[LTR_retriever: accurately identifies and annotates LTR retrotransposons and use LAI to evaluates the continuity of genome assemblies.]]> LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, and/or MGEScan-LTR and generating non-redundant LTR-RT library for genome annotations.

By default, the program will generate whole-genome LTR-RT annotation and the LTR Assembly Index (LAI) for evaluations of the assembly continuity of the input genome. Users can also run LAI separately (see Usage).

Address of the bookmark: https://github.com/oushujun/LTR_retriever

]]> Neel https://bioinformaticsonline.com/news/view/40416/5700-year-old-human-genome Thu, 19 Dec 2019 11:22:18 -0600 https://bioinformaticsonline.com/news/view/40416/5700-year-old-human-genome <![CDATA[5700 year-old human genome !]]> A Landmark in genomics, scientists have done something that hasn't been done ever.

Scientists have reconstructed the genome of an ancient human who lived nearly 5,700 years ago in Southern Denmark from the birch pitch- an ancient tar-like substance.

By sequencing the sample, researchers not only discovered the ancient human DNA but also microbial DNA reflecting the oral microbiome of the person who chewed the pitch, along with plant and animal DNA that could be the recent meal she might have consumed.

The DNA sample is comparable in quality to well-preserved teeth and skull bones. The DNA suggests that the chewer was a female, most likely with dark skin, dark brown hair and blue eyes.

]]> Jit