Results for "R"
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Converting BLAST output into CSV
...th all this BLAST output. Generally, that’s the case - you want to...ar enough, there will be one or more parsers written for that...First, we need to get the script. We’ll do that using...If you have Excel installed, try double clicking on it.2331 days ago
Tools for bacterial whole genome annotation
RAST – Web tool...n the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I thin...eudogenes, control regions, direct and inverted repeats, inse...t of KEGG GENES. KOALA (KEGG Orthology And Links Annotation)...2325 days ago
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read...eces of read sequences to generate the final unitig ...5=="-"' AONTself.paf | awk '{print $1}'| sort|uniq > inver...; grep '^S' AONT.gfa |awk '{print ">"$2"\n"$3}' > AONT...2324 days ago
Bioinformatics Web Application Development with Perl
Perl's second wave of adoption came from the growth of the world wide web. Dynamic web pages—the precursor to modern web applicat...that does old things in better ways. In particular, Mojolic...emselves and it's still popular to this day, though PSGI comp...2315 days ago
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
BBSplit internally uses BBMap to map reads to multiple genomes at once, and determine which genome they match b...ously. But if you want to determine whether reads are mouse o...quo;ambig2” flag. The normal use of BBSplit is like Sea..., none of them, one of them, or put in a special "ambiguous"...2308 days ago
- There are several ways you can convert fastq to fasta sequences. Some methods are listed below. Using SED se...WK cat infile.fq | awk '{if(NR%4==1) {printf(">%s\n",subs...STDOUT), report will be printed to STDER...
2299 days ago
PerlOneLiner for Bioinformatician
...----- # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\n" }'perl...scalar(grep{/^$/}<>)'perl -le 'print ~~grep{/^$/}<&...mber PI to 39 decimal placesperl -Mbignum=PI -le 'print PI'...== 1} 1..100; print "@odd"'perl -le '@odd = grep { $_ &...2296 days ago
- To do sam to bam conversion, follow the following commands :-...d to use Code: $ samtools sort file.bam file-sorted foll...by Code: $ samtools index file-sorted.bam in order to get an...s of help giving the correct syntax for that command,
2285 days ago
List of visualization tools for network biology
Network analysis is any structured technique used to mathematically analyze a circuit (a “network”...etworks http://www.cellillustrator.com COPASI Analysis of...neat/ Ondex Data integration and visualization of lar...tion and visualization of interactive large, dense graphs ht...2282 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing final results but also for improving analysis protocols,...figure of genomes. Following are the list of genome alignment...equencing technologies. Low- or high-depth read pileups and e...arge heterogeneous datasets, providing a smooth and intuitive...2277 days ago
