Comment on "URMAP, an ultra-fast read mapper"
...reads because decompression is typically more expensive than the additional file...ncompressed file. OptionsThe FASTQ filename is specified following -map. Use "-".../dev/stdout or "-" (minus sign) if you want to pipe output to another program. T...1299 days ago
Comment on "Sibelia: A comparative genomics tool"
...with "fine" parameters set, type: Sibelia -s fine Helicoba...m [5, 6]. Note that you can specify multiple FASTA files, jus...me synteny block. Genomes permutations ------------------...s are from negative strand respectively. Note that this graph...1301 days ago
Comment on "Basic command-line to run BLAST"
Original paper https://www.sciencedirect.com/science/article/pii/S00222836058036021311 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...d to do is to combine the reads into a single file, for gzipped files, this can be done with zcat, or for unzipped files cat. Ex. $...y removing the combined fasta file, and re-zipping any unzipped files. Then download the out...1353 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...assembly based on incongruently mapped reads. It is heavily based o...urious sites to form smaller (but hopefully correct) contigs. Reapr...eapr needs, is a list of all “perfect” reads. This is re...pping called <assembler>_perfect. This should take about...1353 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-scope1358 days ago
1377 days ago
Comment on "How to install Perl modules manually, using CPAN command, and other quick ways"
#To install perl modules perl -MCPAN -e shell # go to CPAN install modeinstall Bundle::CPAN # update CPANreload cpaninstall Set::Scalar1397 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
halSynteny program makes it possible to speed up the computations by over two times in comparison with SatsumaSynteny2, another popular tool. Such high efficiency was attained by im...1427 days ago
Comment on "AutoDock Vina: an open-source program for doing molecular docking."
AutoDockFR (or ADFR in short) is a protein-ligand docking program developed in the Sanner laboratory at Scripps Research under the AutoDock umbrella. https://ccsb.scripps.edu/adfr/1438 days ago