Comment on "URMAP, an ultra-fast read mapper"
map command Maps unpaired reads to a reference genome. The reference genome is stored as a UFI file created by the make_ufi command. The original FASTA file for the refer...1286 days ago
Comment on "Sibelia: A comparative genomics tool"
...n "Output description" for detailed depiction of the output fo...at sequences that do not contain any synteny blocks instances...ased index of the first base pair of the instance 4. End -- o...Sibelia" plots only blocks obtained after the last stage. You...1287 days ago
Comment on "Mugsy: multiple whole genome alignment tool"
...ch input filename will be used as the genome name in the output files (eg. genome1 from genome1.fsa). Header lines in the FASTA files should not contain ':' or '-' to avoid parsing...1288 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
Using KAT again (You will need the modules: KAT/2.1.1 and gnuplot/4.6.5) – we can plot the kmer content of the assembly compared to the kmer content of...1340 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...ool we need is reapr smaltmap which creates a bam file of read-pair mappings. Do the same thing...ten minutes. There are several checks you can do after running Reapr (detailed here) but for now we&...1340 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-scope1345 days ago
1364 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/bioinformatics1386 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
...kes it possible to speed up the computations by over two times in comparison with SatsumaSynteny2, another popular tool. Such high efficiency was attained by implementing a mathemat...1414 days ago
Comment on "Setting up autoConTAMPR !"
.../archive.ubuntu.com/ubuntu/ trusty/main libsub-uplevel-perl all 0.24.../archive.ubuntu.com/ubuntu/ trusty/main libterm-readkey-perl amd64 2...u6.14) ...Removing intermediate container 7adc9dbdb955 --->...sv_cb.t ............ okt/fields_containing_0.t .. okt/rt99774.t .......1445 days ago