BOL: Related items

PhD position in Translational Medicine

Sat, 15 Feb 2020 06:07:19 -0600

https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/wissenschaftliche-r-mitarbeiter-in/phd-position-translational-medicine-129981.html?suid=1b510358c7578e8f75cf04a464fc21a404a574ca

Essential experience / qualifications:
Master / Diploma in Biology, Biochemistry, Molecular Medicine or similar; solid knowledge of molecular and cell biological techniques; good English knowledge

Applications:
Please send your application (including CV, letter of motivation, contact information of two references, and list of publication) by 13.03.2020 at the latest to:

Universitätsklinikum Erlangen
Chirurgische Klinik
Translational Research Center
Prof. Dr. rer. nat. Michael Stürzl
Schwabachanlage 12
91054 Erlangen
E-Mail: michael.stuerzl@uk-erlangen.de

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

Pollux: platform independent error correction of single and mixed genomes

Jit — Fri, 19 May 2017 09:41:27 -0500

Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0435-6

Address of the bookmark: https://github.com/emarinier/pollux

Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

Jit — Tue, 26 Apr 2016 12:18:49 -0500

Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ideogramoutput architecture, where the patterns are represented with several HSV values (only value varies). The method can perform both in small- and large-scale. Nevertheless is more directed to large-scale since that the main aim of the research is to know where the large-scale [chromosomal by chromosome] of several primates was equal/different, having at a glance a map of the entire genomes.

Address of the bookmark: http://bioinformatics.ua.pt/software/smash/

Spines

Jit — Mon, 28 Nov 2016 05:33:26 -0600

Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

Address of the bookmark: https://www.broadinstitute.org/genome-sequencing-and-analysis/spines

Harvest

Jit — Tue, 31 Jan 2017 10:57:56 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

J-Circos

Shruti Paniwala — Fri, 17 Feb 2017 09:06:54 -0600

Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.

Address of the bookmark: http://www.australianprostatecentre.org/research/software/jcircos

DIAMOND

Jit — Thu, 27 Apr 2017 04:21:54 -0500

DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

More at file:///home/urbe/Downloads/diamond_manual.pdf

http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html

Address of the bookmark: https://github.com/bbuchfink/diamond

progressiveCactus

Abhimanyu Singh — Thu, 18 May 2017 05:29:29 -0500

Progressive Cactus is a whole-genome alignment package.

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

https://github.com/glennhickey/progressiveCactus

Address of the bookmark: https://github.com/glennhickey/progressiveCactus

SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists

Neel — Thu, 23 Nov 2017 17:15:52 -0600

This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit, Windows Vista 32bit, Windows 2008 Server, Windows 7 32bit and 64bit, Ubuntu 10.04 64bit, Ubuntu 10.10 64bit, and gentoo AMD64.

The corresponding publication can be found here:

B. Voss*, M. Hanselmann*, B.Y. Renard, M.S. Lindner, U. Köthe, M. Kirchner, F.A. Hamprecht (2011). SIMA: Simultaneous Muliple Alignment of LC/MS Peak Lists, Bioinformatics 27(7):987-993. [doi] [techreport]

Address of the bookmark: https://hciweb.iwr.uni-heidelberg.de/hci/softwares/sima