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kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2541 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the...
By Rahul Nayak 1822 days agopypi.org - The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also...
Sample bandage input file for visual analysis
By Jit 1416 days agoSample bandage input file for visual analysis ...Bioinformatics Scientist, Production Bioinformatics @ South San Francisco, CA
wist is looking for a Bioinformatics Scientist to join our Production Bioinformatics Team. You will work alongside research scientists, software engineers and data scientists to further deliver on our mission to expand access to best-in-class...Job offer for a postdoctoral researcher in genomics / bioinformatics (2 years)
Ongoing research in the group of Karine Van Doninck involves topics at the core of evolutionary biology, including the evolution of sex, genome maintenance, recombination and extreme stress resistance on different eukaryotic systems, including...Bioinformatics 101 - Running BLAST
By Poonam Mahapatra 4098 days agoHow to format the database for BLAST, run the command, view the output file, and use BioPerl and Perl to parse the output. By David Francis, Ohio State University. Delivered live at the Tomato Disease Workshop 2010. For more information, please...assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference...
By Jit 2353 days agohttp://assemblytics.com/ - Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip...Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome...
By Jit 1984 days agogithub.com - Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding...VCF Compare !
By Rahul Nayak 1038 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...Orione – a web-based framework for NGS analysis in microbiology
By Martin Jones 3775 days agohttp://orione.crs4.it/ - End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that...
