BOL: Related items

MyCC: Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

Jit — Fri, 03 Mar 2017 08:34:23 -0600

MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments.

More at http://www.nature.com/articles/srep24175

Address of the bookmark: https://sourceforge.net/projects/sb2nhri/files/MyCC/

MaxBin: software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

Jit — Mon, 06 Mar 2017 04:03:38 -0600

MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page.

Users can use MEGAN or similar software on MaxBin bins to find the taxonomy of each bin after the binning process is finished.

https://academic.oup.com/bioinformatics/article/32/4/605/1744462/MaxBin-2-0-an-automated-binning-algorithm-to

The most recent version of MaxBin is 2.2, which supports the analysis of coassemblies of multiple samples. It is available at this JBEI downloads sites as well as MaxBin and MaxBin 2.0 sourceforge sites.

Address of the bookmark: http://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html

GroopM: Metagenomic binning toolset

Jit — Tue, 07 Mar 2017 08:59:45 -0600

GroopM is a metagenomic binning toolset. It leverages spatio-temoral
dynamics (differential coverage) to accurately (and almost automatically)
extract population genomes from multi-sample metagenomic datasets.

GroopM is largely parameter-free. Use: groopm -h for more info.

For installation and usage instructions see : http://ecogenomics.github.io/GroopM/

Address of the bookmark: https://github.com/ecogenomics/GroopM

NCBI Prokaryotic Genome Annotation Pipeline

Jit — Tue, 16 May 2017 08:56:03 -0500

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. You can find a more detailed description of the new version of the pipeline in NCBI Handbook chapter. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

ASAR: Advanced metagenomic Sequence Analysis in R

Jit — Mon, 09 Jul 2018 05:20:50 -0500

An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

Scripts for the analysis of HGT in genome sequence data.

Jit — Wed, 29 Nov 2017 16:44:10 -0600

Scripts for the analysis of HGT in genome sequence data

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

GIGGLE: a search engine for large-scale integrated genome analysis

Jit — Wed, 10 Jan 2018 03:10:45 -0600

GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.

https://www.nature.com/articles/nmeth.4556

Address of the bookmark: https://github.com/ryanlayer/giggle

Bio7: an integrated development environment for ecological modeling, scientific image analysis and statistical analysis

Nidhi Rajput — Fri, 07 Feb 2020 23:32:24 -0600

The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

https://bio7.org/about/

Address of the bookmark: https://bio7.org/home-2/

DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms

Neel — Wed, 25 Nov 2020 19:51:38 -0600

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

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

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