Results for "B"
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Converting BLAST output into CSV
...l matches, or do a reciprocal BLAST, or something. As with m...is popular enough, there will be one or more parsers written...squo;s conclude this tutorial by converting the BLAST output...;re looking to run the script blast/blast-to-csv.py using Pyt...2395 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotatio...essing a larger data volume. NCBI's annotation pipeline...omes and to create genome databases. It identifies repeats, a...2389 days ago
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembler for...uts an assembly graph in the GFA format. Different...s largest than 10, 20 and 30 kb) minidot -f 5 -m 30000 AON...; AONT_miniasm_self10000.eps Njoy the assembly !2388 days ago
Bioinformatics Web Application Development with Perl
...he growth of the world wide web. Dynamic web pages—the precursor to...yonder, declaring every variable at the top of the program,...lications. Mojolicious The Mojolicious (Mojo) fra...hanisms exist to meet various business needs which also suppo...2379 days ago
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
BBSplit internally uses BBMap to map reads to multiple...ere, reads mapping to it will be mapped ambiguously. But if y...uman, only whether they are ambiguous between human and mouse...e from which reference file. BBSplit is a tool that bins rea...in 2 files, you would do this:bbsplit.sh in1=reads1.fq in2=re...2372 days ago
- ...equences. Some methods are listed below. Using SED sed can be used to selectively...can linerize every 4 lines in a tabular format and print first an...fastq -outseq reads.fasta awk can be used for conversion...uences. [-v] = Verbose - report number of sequenc...
2363 days ago
PerlOneLiner for Bioinformatician
...ILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\n" }'perl -pe '$_...Replace each field with its absolute valueperl -alne 'print...# Generate and print the alphabetperl -le 'print a..z'perl -l...t all lines that contain a numberperl -ne 'print if /\d/' #...2360 days ago
- To do sam to bam conversion, follow the following commands :- Code: $ samtools view -b -S file.sam > file.bam Then you... Code: $ samtools sort file.bam file-sorted followed by...: $ samtools or samtools followed by the name of one of the samto...
2349 days ago
List of visualization tools for network biology
...erconnected components). The Network analysis provides the ability to quantify associations...oftware http://magnet.systemsbiology.net/software/Dizzy/ Dy...cs.tau.ac.il/pivot/ ProCope Prediction and evaluation...and proteins http://stitch.embl.de/ STRING Protein interac...2346 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing final results but also for improving analysis...ualization tools, which could be useful for analysis and ...ftware/artemis/ DNannotator Annotation web toolkit fo...rsquo; (pip) http://pipmaker.bx.psu.edu/pipmaker/ PileLineG...2341 days ago
