Comment on "URMAP, an ultra-fast read mapper"
...genome is stored as a UFI file created by the make_ufi command...ed FASTQ format. It is generally faster to use uncompressed reads be...t mapping algorithm which is ~3x faster but somewhat less accurate....tdout will not work because urmap attempts to create the file. Exam...1281 days ago
Comment on "Sibelia: A comparative genomics tool"
...tput format. The "far" parameters set can be used for analysi...irectory. Setting this parameter will change output directory...Genome line -- sequence of synteny blocks instances as they ap...y stage produces it's own synteny blocks. You can get blocks...1283 days ago
Comment on "Mugsy: multiple whole genome alignment tool"
...nome3.fasta This example will align three genomes and output a file /data/output/mygenomes.maf. The --directory setting is also used for storing temporary files during the run.T...1284 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...t/4.6.5) – we can plot the kmer content of the assembly compared to the kmer content of the read set. The first...e will now use kat comp to create a kmer content comparison. Us...en download the output files to you computer using scp and look...1335 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...up contigs/scaffolds at spurious sites to form smaller (but hopeful...ck <assembly.fasta> will tell you if everything’s o...sp;to get information on how to create a perfect mapping file, and c...with the original assembly to generate a quast report. How does the...1335 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-scope1340 days ago
1359 days ago
Comment on "Important Journals, Blogs and Forums for Bioinformaticians"
International Journal of Bioinformatics Research and Applications Indexed in Scopus (Elsevier) Academic OneFile (Gale) ACM Digital Library Current Awareness in Biological Sciences (Elsevier) Chemical Abstracts (CAS)1361 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::Scalar1379 days ago
Comment on "FRODOCK 2.0: fast protein–protein docking server"
A web applet for browsing protein-protein interactions was implemented. It enables the display of interaction relationships, based upon neighboring distance and biological function. Availability: The Java applet is available at http://www.charite.de/bioinformatics1381 days ago