Comment on "Ten International Scholarships for Indian Biotechnology and Bioinformatics Students"
Useful books for Indian scholarships https://indiabioscience.org/media/articles/GRANTS-BOOK-FINALVer_09111.pdf1310 days ago
Comment on "Important Journals, Blogs and Forums for Bioinformaticians"
IEEE Transactions on Knowledge and Data Engineering accepts bioinformatics and algorithms manuscripts https://www.computer.org/csdl/journal/tk1327 days ago
Comment on "URMAP, an ultra-fast read mapper"
map command Maps unpaired reads to a reference genome. The reference genome is stored as a...essed FASTQ format. It is generally faster to use uncompresse...-" (minus sign) to get input from a pipe. If the reads are gz...veryfast option specifies a variant mapping algorithm which i...1340 days ago
Comment on "Sibelia: A comparative genomics tool"
...is assumed that "Sibelia" is properly installed and the director...any synteny blocks instances are not shown on these diagrams....eny block Note that all coordinates are given relatively t...hat only bifurcations in the graph are plotted and non-bran...1342 days ago
Comment on "Mugsy: multiple whole genome alignment tool"
Set up the environment bash source /path/to/install/mugsyenv.sh Run mugsy... mugsy --directory /data/output --prefix m.../output/mygenomes.maf. The --directory setting is also used fo...oid parsing problems. View or parse MAF output The outpu...1342 days ago
Comment on "Basic command-line to run BLAST"
Original paper https://www.sciencedirect.com/science/article/pii/S00222836058036021352 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
....6.5) – we can plot the kmer content of the assembly compared to the kmer content of the...the reads into a single file, for gzipped files, this can be do...t comp --help to get help for the program, then create a co...nation would look like in the kmer plot? What can the kmer grap...1394 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
Reapr is a tool trying to find explicit errors in the assembly based on incongruently mapped reads. It is hea...r runs pretty slowly, sadly, Reapr is a bit fuzzy with conti...with the contig names. If you run into any problems, run ...The next tool we need is reapr smaltmap which creat...1394 days ago
Comment on "Important Journals, Blogs and Forums for Bioinformaticians"
Biology Direct journals accept short notes/ application notes https://biologydirect.biomedcentral.com/submission-guidelines/aims-and-scope1399 days ago
Comment on "Important Journals, Blogs and Forums for Bioinformaticians"
NAR Web server accept tools https://academic.oup.com/nar/issue/43/W11399 days ago