BOL: Related items

HGA

Jit — Tue, 29 Nov 2016 07:25:53 -0600

HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler (Velvet or SPAdes in this version) and using a given kmer size. 3. Merging all the assemblies of the partition. 4. Combining all the assemblies of the partition (using velvet with kmer value of 31). 5. Finaly, re-assembling the whole dataset with the merged contigs or the combined contigs, using a given kmer size.

https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA

Address of the bookmark: https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation

Neel — Thu, 15 Dec 2016 05:47:35 -0600

MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requires minimal programming skills. High-quality prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de novo assemblers and contig integration software. Produces more contiguous assemblies, higher N50 values and lower number of contigs.

More at https://sourceforge.net/projects/sb2nhri/files/MyPro/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S0167701215001207

Randomness and Probability

Jit — Tue, 08 Nov 2016 07:17:32 -0600

Randomness and Probability

Randomness and probability are two differnet concepts: probaility is a measure (according to measure theory) which measures the randomness. Randomness is the object to be measured by probability. For example, probability is a mapping from randomness to the real number between 0 and 1. The similar examples are that the entropy measures the uncertanity; product of length and width measures the area of rectangle etc.

Please see “A mathematical theory of ability measure” by N. Kong ets for more examples to answer this question.

Bioistats Online course

Abhimanyu Singh — Thu, 10 Nov 2016 04:22:51 -0600

One of our primary focuses will be to develop an understanding of the various ways in which we can assign a probability to some chance event. We'll also learn the fundamental properties of probability, investigate how probability behaves, and learn how to calculate the probability of a new chance event.

This book is handy understanding basic concepts.

Address of the bookmark: https://onlinecourses.science.psu.edu/stat414/node/287

HTSlib

Jit — Wed, 15 Mar 2017 11:38:05 -0500

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
HTSlib: A C library for reading/writing high-throughput sequencing data

Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

Address of the bookmark: http://www.htslib.org/

gbtools: Interactive Visualization of Metagenome Bins in R

Jit — Sun, 26 Mar 2017 15:41:31 -0500

We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of annotations, including taxonomic assignments from conserved marker genes or SSU rRNA genes, can be imported simultaneously; users can choose which annotations to plot. Bins can be manually defined from plots, or be imported from third-party binning tools and overlaid onto plots, such that results from different methods can be compared side-by-side. gbtools reports summary statistics of bins including marker gene completeness, and allows the user to add or subtract bins with each other.

Tool at https://github.com/kbseah/genome-bin-tools

Address of the bookmark: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01451/full

DeCoSTAR - Detection of Co-evolution

Jit — Fri, 14 Apr 2017 06:27:25 -0500

DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.
Ancestral genes or domains are deduced from reconciled gene trees in a context of birth, speciation, duplication, loss, transfer, which are either given as input or computed with the ecceTERA package, to which DeCoSTAR is integrated. DeCoSTAR constructs parsimonious scenarios of gains and breakages of adjacencies, and contains in particular all the features of previous software DeCo, DeCoLT, ArtDeCo and DeClone. It provides statistical supports on ancestral adjacencies, or the possibility to handle badly assembled genomes.
DeCoSTAR is able to reconstruct the histories of domains inside genes, including gene fusion and fission events, as well as ancestral genome structures for dozens of whole genomes from all kingdoms of life in a few minutes.

Address of the bookmark: http://pbil.univ-lyon1.fr/software/DeCoSTAR/

UpSetR Shiny App!

Jit — Fri, 14 Apr 2017 06:19:54 -0500

UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.

To begin, input your data using one of the three input styles.

"File" takes a correctly formatted.csv file.
"List" takes up to 6 different lists that contain unique elements, similar to that used in the web applications BioVenn (Hulsen et al., 2008) and jvenn (Bardou et al., 2014)
"Expression" takes the input used by the venneuler R package (Wilkinson, 2015)

Address of the bookmark: https://gehlenborglab.shinyapps.io/upsetr/

DIYA: a bacterial annotation pipeline for any genomics lab

Jit — Fri, 30 Jun 2017 08:48:26 -0500

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

http://gmod.org/wiki/Diya

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

CLA: Contig-Layout-Authenticator

Jit — Fri, 05 May 2017 05:58:36 -0500

To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.

Script https://sourceforge.net/projects/c-l-authenticator/files/

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155459