BOL: Related items

QUAST: quality assessment tool for genome assemblies

Jitendra Prajapati — Wed, 06 Apr 2016 18:23:33 -0500

QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.
It can works both with and without a given reference genome.
The tool accepts multiple assemblies, thus is suitable for comparison.

More at http://bioinf.spbau.ru/quast

http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

SPAdes

Abhimanyu Singh — Tue, 19 Apr 2016 08:37:08 -0500

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau.ru/en/spades.

Manual at http://spades.bioinf.spbau.ru/release3.7.1/manual.html

Address of the bookmark: http://bioinf.spbau.ru/spades

GATB : Genome Analysis Toolbox with de-Bruijn graph

Jit — Thu, 28 Apr 2016 11:16:51 -0500

The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes).

More at https://gatb.inria.fr/

Address of the bookmark: https://gatb.inria.fr/

GAEMR

Jit — Tue, 14 Jun 2016 06:18:37 -0500

The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete analysis report, or executed individually to generate specific charts and tables. GAEMR standardizes input by converting a variety of read types to Binary Alignment Map (BAM) format, allowing a single input format to be entered into GAEMR’s analysis pipeline, hence enabling the generation of standard reports.

GAEMR’s analysis philosophy is centered on contiguity, correctness, and completeness -- how many pieces in an assembly composed of, how well those pieces accurately represent the genome sequenced, and how much of that genome is represented by those pieces. By performing over twenty different analyses based on these principles, GAEMR gives a clear picture of the condition of a genome assembly.

Address of the bookmark: https://www.broadinstitute.org/software/gaemr/

Understanding PacBio

Jitendra Narayan — Fri, 24 Feb 2017 10:17:36 -0600

This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you get started with your data processing, as well as information for specialized applications.

Training Resources:

Specialized Applications:

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

Minia

Jit — Thu, 08 Dec 2016 05:07:00 -0600

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

Download

Minia 2.0.7 Linux 64-bits binaries (Source code) (Legacy codebase)

For the impatient

A typical Minia command line looks like:

./minia -in reads.fa -kmer-size 31 -abundance-min 3 -out output_prefix

Type

./minia

for a quick explanation of the parameters.

For more information, refer to the manual.

KmerGenie can be used to determine the best k-mer size, minimum abundance of correct k-mers, and genome size estimation for your dataset.

Address of the bookmark: http://minia.genouest.org/

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

Jit — Mon, 06 Feb 2017 04:45:37 -0600

DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

Address of the bookmark: http://www.ub.edu/dnasp/

Ideoplot

Shruti Paniwala — Mon, 13 Feb 2017 09:47:32 -0600

Simple ideogram plotting and annotation in R.

Basic usage:

Rscript Ideoplot.R --heatmap hm.bed --annotate annotations.bed --out ideogram.pdf
-or-
Rscript Ideoplot.R --annotate annotations.bed

Options
  --ideobed, i      A bed file of reference contig lengths/chromosome names
  --heatmap, -h     Fill chromosomes with normalized heatmap
                   (described below)
  --annotate, -a    Add character annotations.
  --out, -o         PDF output name.
  --stripes, -s     Specify a file containing the layout of the
                    annotations (description below)
  --bars, -b        Add track annotations
  --reference, -f   Either hg19, or hg38
  --topdown, r      Flag, when set, flips the orientation (P arms
                    drawn on top).

Address of the bookmark: https://github.com/mchaisso/Ideoplot

GenomeComp

Jit — Fri, 17 Feb 2017 08:38:32 -0600

GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or strains.

It can be easily used to compare, parsing and visualize large genomic sequences, especially closely related genomes such as inter-species or inter-strains. In addition, it can also show other sequence features like repeat sequence distributions in one whole-genome DNA sequence by comparing the genome to itself.

It is a stand-alone graphical user interface (GUI) program which runs on Linux, Unix, Mac OS X (tested on version 10.2.4 only) and Microsoft Windows platforms and is written in Perl/Tk.

Address of the bookmark: http://www.mgc.ac.cn/GenomeComp/

Laj: viewing and manipulating the output from pairwise alignment programs

Abhimanyu Singh — Wed, 01 Mar 2017 08:35:40 -0600

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.

The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for "Local Alignments with Java". Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.

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