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Converting BLAST output into CSV
Suppose we wanted to do something with all this BLAST output. Generally, that’s the case...t. If the program is popular enough, there will be one or mor...into a spreadsheet format, using a Python script. Firs...s a spread-sheet like list of names and e-values. To save thi...2389 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annot...Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; ...them; (ii) IMAGE uses paired-end reads to extend contigs and...2383 days ago
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembler for noisy l...ssembly graph in the GFA format. Different from mai...t than 10, 20 and 30 kb) minidot -f 5 -m 30000 AONTself.pa...iniasm_self10000.eps Njoy the assembly !2382 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 applications—were easy to create wi...base access since its invention. Its design allows it to prov...raries make it more powerful and pleasant than ever....2373 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 best...s are mouse or human, it does not matter whether they map amb...ence, or splitting the reads into multiple output files, one...was contaminated with e.coli and salmonella, you could do thi...2366 days ago
- ...There are several ways you can convert fastq to fasta sequences....nes from a file, so if you print the first and 2rd line of ev...AWK cat infile.fq | awk '{if(NR%4==1) {printf(">%s\n",sub...report will be printed to STDERR. [-z]...
2357 days ago
PerlOneLiner for Bioinformatician
FILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\n" }'perl -pe '$_ .= "...'perl -MList::Util=shuffle -alne 'print join " ", shuffle @F'...: n*m/gcd(n,m)perl -le '$a = $n = 20; $b = $m = 35; ($m,$n) =...f eof' # Print the last 10 lines of a file (emulate tail -10...2354 days ago
- To do sam to bam conversion, follow the following commands :- Code: $ sa...b -S file.sam > file.bam Then you will need to use ...followed by Code: $ samtools index file-sorted.bam in ord...the correct syntax for that command,...
2343 days ago
List of visualization tools for network biology
Network analysis is any structured technique used to mathematically analyze a circuit (a “netw...://www.copasi.org/ Cytoscape Network visualization an...a.mshri.on.ca/osprey/servlet/Index Pajek Analysis and...n networks across species to infer protein complexes that are...2340 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing final results but also for i...pelines allows the optimization of parameters, which leads to...ce, and also its six-frame translation http://www.sanger.ac....MultiPipMaker Computes alignments of similar regions in tw...2335 days ago
