Results for "C"
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Converting BLAST output into CSV
...ut. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST,..., the text output is in some specific format. If the program is...n from the output. Let’s conclude this tutorial by conve...placed the files in /root/ngs-scripts/, and you’re looki...2350 days ago
Tools for bacterial whole genome annotation
...ity annotation in a flash, which is particularly useful if yo...ine is designed to annotate bacterial and archaeal genomes (c...wnload or use outside of the NCBI environment. BEACON (autom...produces ab-initio gene predictions and automatically synthe...2345 days ago
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembler for noisy long...eads. It takes all-vs-all read self-mappings (typically by minimap) as input...om mainstream assemblers, miniasm does not have a consensus step. It simply conca...2343 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 crea...programming with Perl (see Mechanize or LWP or Mojo::UserAge...to your database based on the concept of queries and results....2335 days ago
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
...eads to multiple genomes at once, and determine which genome they match best. This...n human and mouse. BBSplit tracks this additional ambiguity i...onal information regarding which sequences came from which re...=reads1.fq in2=reads2.fq ref=ecoli.fa,salmonella.fa basename=...2328 days ago
- ...There are several ways you can convert fastq to fasta sequence...ry 4 lines, you get the sequence header and sequence needed f...le in the FASTX-toolkit that scales really well with the huge...s another option using a tool called seqtk seqtk seq -a...
2318 days ago
PerlOneLiner for Bioinformatician
FILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl...er of lines in a file that match a pattern (emulate grep -c)p...rint e' # Print UNIX time (seconds since Jan 1, 1970, 00:00:...ZA-Mn-za-m/' file # Base64 encode a stringperl -MMIME::Base6...2315 days ago
- To do sam to bam conversion, follow the following commands :- Code: $ samtools view -b -S file.sam >...bam Then you will need to use Code: $ samtools sort file.bam...an indexed file.If you just type Code: $ samtools or samtool...
2304 days ago
List of visualization tools for network biology
...work analysis is any structured technique used to mathematically analyze a circuit (a “network&rdquo...n be used to identify dynamic communities in networks https:...w.bio.ifi.lmu.de/Complexes/ProCope/ ProViz Visualizat...l for exploring networks that change over time or space http...2301 days ago
List of visualization tools for genome alignments
...ptimization of parameters, which leads to better results. But...nment visualization tools, which could be useful for analysis...allows visualization of sequence features, next-generation se...short read alignment, identification of genetic variation and...2297 days ago
