BOL: Related items

ShRec3D

Jitendra Narayan — Thu, 25 Dec 2014 23:14:52 -0600

ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C (http://www.ncbi.nlm.nih.gov/pubmed/19815776).

There are two options to run ShRec3D (on linuX only so far): the first one uses the Matlab complier runtime environment (MCR), the second one doesn't need any other library to be installed but only works with the latest versions of Linux (equivalent to Fedora 19 and above).

Address of the bookmark: https://sites.google.com/site/julienmozziconacci/#TOC-Downloads

Nicolas Corradi Lab

Tue, 26 May 2015 16:19:02 -0500

The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance.
To achieve this goal, our team combines the power of next generation DNA sequencing and bioinformatics with molecular biology and experimental procedures.

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

Rosalind Problem Solution with Perl

Jit — Tue, 09 Jun 2015 23:35:18 -0500

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

Bioinformatics Textbook Track

Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track

I will provide solution of all the Rosalind problem with Perl for community.

Check out the right sidebar for more links ...

Pilon

Rahul Nayak — Mon, 08 Feb 2016 15:56:18 -0600

Pilon is a software tool which can be used to:

Automatically improve draft assemblies
Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.

Jit — Tue, 26 Apr 2016 11:38:10 -0500

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.

Canu is a hierachical assembly pipeline which runs in four steps:

Detect overlaps in high-noise sequences using MHAP
Generate corrected sequence consensus
Trim corrected sequences
Assemble trimmed corrected sequences

Read the documentation

New release https://github.com/marbl/canu/releases

Address of the bookmark: https://github.com/marbl/canu

YASS :: genomic similarity search tool

Jit — Mon, 02 May 2016 09:26:00 -0500

YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to local alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step (as provided for example by iedera).

Main features of YASS are:

multiple, possibly overlapping seeds and a new hit criterion to ensure a good sensitivity/selectivity trade-off
transition-constrained spaced seeds to improve sensitivity (transition mutations are purine to purine [A<->G] or pyrimidine to pyrimidine [C<->T])
using different scoring schemes with bit-score and E-value evaluated according to the sequence background frequencies
parameterizable output filter for low complexity repeats
reporting of various alignment statistical parameters (mutation bias along triplets, transition/transversion)
post-processing step to group gapped alignments

Address of the bookmark: http://bioinfo.lifl.fr/yass/

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

methylKit

Jit — Fri, 03 Jun 2016 10:09:29 -0500

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

Address of the bookmark: https://github.com/al2na/methylKit

4DGenome

Jitendra Narayan — Mon, 04 Jul 2016 00:44:55 -0500

Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data cover both high throughput datasets and individiual focused studies.

All interaction data are freely available in a standardized file format. Records can be queried by genomic regions, gene names, organism, and detection technology.

Address of the bookmark: http://4dgenome.research.chop.edu/

vcfR

Archana Malhotra — Fri, 19 Aug 2016 07:38:24 -0500

Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files are typically intended to be post-processed (i.e., filtered) as an attempt to remove false positives or otherwise problematic sites. The R package vcfR provides tools to facilitate this filtering as well as to visualize the effects of choices made during this process.

Address of the bookmark: https://cran.r-project.org/web/packages/vcfR/vignettes/visualization_1.html