BOL: Related items

mScaffolder: A comparative genome scaffolding tool

Jit — Fri, 15 Jun 2018 04:48:01 -0500

A comparative genome scaffolding tool based on MUMmer

mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to the reference genome. Please send your questions and comments to mchakrab@uci.edu.

Citation https://www.nature.com/articles/s41588-017-0010-y

Address of the bookmark: https://github.com/mahulchak/mscaffolder

Genome U-Plot: a whole genome visualization

Rahul Nayak — Fri, 13 Jul 2018 19:50:41 -0500

Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities.

https://github.com/gaitat/GenomeUPlot

Address of the bookmark: https://github.com/gaitat/GenomeUPlot

GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences

Jit — Fri, 28 Sep 2018 09:35:10 -0500

GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:

Step 1. Run mugsy to get multiple sequence alignment results.
Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permutations.
Step 4. Generate pairwise genome rearrangement scenarios and find repeats at the breakpoints of each rearrangement events.

https://github.com/DanwangJessica/GRSR

Address of the bookmark: https://github.com/DanwangJessica/GRSR

Software developed in pevsner lab

Robert M Willioms — Mon, 06 Oct 2014 12:41:26 -0500

DRAGON: Database Referencing of Array Genes Online

SNOMAD: Standardization and Normalization of Microarray Data

SNPduo: SNP Analysis Between Two Individuals

SNPtrio: Analyzing and Visualizing and Inheritance Patterns in Trios

SNPscan: Data Analysis and Visualization of SNP Data

pediSNP: Analyze SNP Data From a Pedigree of Two Generations

kcoeff: Calculate Cotterman Coefficients of SNP Genotype Data

triPOD: Detects chromosomal abnormalities in parent-child trio-based microarray data

Address of the bookmark: http://pevsnerlab.kennedykrieger.org/php/?q=software

deepTools

Martin Jones — Sat, 08 Nov 2014 15:02:08 -0600

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.

Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full

Source Code and Wiki: https://github.com/fidelram/deepTools/wiki

Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows

RagTag: a collection of software tools for scaffolding and improving modern genome assemblies

Jit — Sat, 11 Sep 2021 00:28:14 -0500

RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

Homology-based misassembly correction
Homology-based assembly scaffolding and patching
Scaffold merging

Address of the bookmark: https://github.com/malonge/RagTag

VCF Compare !

Rahul Nayak — Wed, 19 Jan 2022 10:30:14 -0600

compare two BWA mapping methods with the online hg18-mapped data

We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam>, aligned to the b36/hg18 reference genome)

Address of the bookmark: https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare

Rosalind Bioinformatics problems !!!

Abhi — Thu, 18 Dec 2014 10:32:48 -0600

Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

http://rosalind.info/problems/list-view/

Address of the bookmark: http://rosalind.info/problems/list-view/

fragScaff: Genome Assembly with Contiguity Preserving Transposition

Jit — Mon, 14 May 2018 04:28:14 -0500

Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. This software, fragScaff, leverages coincidences between the content of different pools as a source of contiguity information for scaffolding de novo genome assemblies. FragScaff is complementary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.

Further information about fragScaff, including source code, is available at:https://sourceforge.net/projects/fragscaff/files.

Manuscript describing fragScaff was published as: Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, L Gunderson K, Steemers FJ, Shendure J#. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Research 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. PubMed PMID: 25327137.

Address of the bookmark: https://sourceforge.net/projects/fragscaff/files/

LASTZ

Abhi — Mon, 18 Apr 2016 04:41:55 -0500

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

More at http://www.bx.psu.edu/~rsharris/lastz/

Thesis: http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf

Address of the bookmark: http://www.bx.psu.edu/~rsharris/lastz/