BOL: Related items

Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data

Jit — Thu, 11 Feb 2021 21:39:05 -0600

Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz v1.2.7 for Linux x86_64 system. If you could not run it (which is usually caused by low version of libc++ or libz library) or you want to build a version optimized for your system, you can re-compile the programs:

user@linux$ make clean && make

Address of the bookmark: https://github.com/hellosunking/Ktrim

dcGOR

Martin Jones — Sat, 08 Nov 2014 14:54:28 -0600

An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1003929). The package is distributed as part of CRAN (http://cran.r-project.org/package=dcGOR), and also at GitHub for version control.

The dedicated website is available in http://supfam.org/dcGOR, from which several demos are also provided:

1. Analysing SCOP domains: http://supfam.org/dcGOR/demo-Fang.html

2. Analysing Pfam domains: http://supfam.org/dcGOR/demo-Basu.html

3. Analysing InterPro domains: http://supfam.org/dcGOR/demo-Customisation.html

Andi

Jit — Fri, 13 May 2016 05:16:35 -0500

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full

Bpipe - a tool for running and managing bioinformatics pipelines

Radha Agarkar — Sat, 21 May 2016 22:42:16 -0500

Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.

January 20th, 2016 - New! Bpipe 0.9.9 released!
Download latest, all
Documentation
Mailing List (Google Group)

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

EasyBuild

Jit — Fri, 27 Jan 2017 16:00:43 -0600

EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
A full list of supported software packages is available here.

Address of the bookmark: https://hpcugent.github.io/easybuild/

HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes

Jit — Wed, 17 Jan 2018 05:03:19 -0600

HGT-Finder:

(i) can be used for HGT detection in both prokaryotes and eukaryotes,

(ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and

(iii) is fully automated (requires minimal human intervention), as well as very easy to install and run.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626719/

SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.

Jit — Sun, 31 May 2020 02:01:14 -0500

SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images.

SynVisio requires two files to run:

The simplified gff file that was used as an input for a McScanX query.
The collinearity file generated as an output by McScanX for the same input query.
Optional track file in bedgraph format to annotate the generated charts.

SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.

Address of the bookmark: https://synvisio.github.io/#/

Panacus : A Counting Tool for Pangenome Graphs

Neel — Fri, 14 Jun 2024 14:42:28 -0500

panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.

panacus supports the following calculations:

coverage histogram
pangenome growth statistics
path-/group-resolved coverage table

Address of the bookmark: https://github.com/marschall-lab/panacus

EXCAVATOR2tool

Bulbul — Wed, 30 Nov 2016 04:09:19 -0600

EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads. Specifically, it improves the precision of calling CNVs overlapping targeted exons from WES data and enlarges the spectrum of detectable CNVs to off-target events.
EXCAVATOR2 can be effectively employed for the identification of CNVs in small as well as large-scale re-sequencing population and cancer studies. Lastly, it’s of particular interest that all WES experiments can be re-analysed using our method with the beneficial effect to identify novelCNVs in extra-exonic regions by having the full-genome CN profile.

Address of the bookmark: https://sourceforge.net/projects/excavator2tool/

RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities

Jit — Mon, 07 Aug 2017 18:49:27 -0500

RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.

Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html.

Address of the bookmark: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp051