Results for "Formats"
Blogs
...enetic tree. It is designed for large-scale studies, including simulation of multiple replicates and outputs sequences into NEXUS, MEGA, or FASTA formats. MySSP has a fairly simple gr...2514 days ago
BBTools for bioinformatician !
...but the syntax is different.------------------------------------------------------------------Randomreads.sh Generate random reads in various formats Code: $ randomr...2254 days ago
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Bookmarks
Java and BioJava Tutorial links
BioJava provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of this bookmark is to provide useful links for bioinformatician. Please add more useful Java and BioJava links here ...3886 days ago
- ...assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/Big...
2992 days ago
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Files
Prepare for Coding Interview !
...ur next coding interview. It's great for recent graduates and has questions and practice materials structured from traditional big tech interview formats.While it does not include the...828 days ago
Pages
Bio++ : C Language libraries for your biological need
...BL or SwissProt,Algorithms for plotting trees, with support for vector formats like SVG, Fig or LaTeX-PGF.So...rage, with several implementations. Support for alignments.Various I/O formats supported: Fasta, Mase, CLust...3931 days ago
Awesome perl frameworks, libraries and software - PART 2
...erules - Test::Apache::RewriteRules - Testing Apache's Rewrite Rules gonzoua/book-tools - perl modules to work with ePUB and FB2 ebook formats fayland/dist-zilla-plugin-pe...2478 days ago
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Top-level pages
Structure of Binary files used for storing sequencing data-bam and sff
...ceforge.net/SAMv1.pdf (from page 12) sff file (for Ion torrent and 454 files): http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff B...3903 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...& Reich, Genome Research 22(5): 939–946. PubMedCentral Data formats, data management, and alignme...ers on bioinformatics and computational genomics. Information on file formats used by the University of Cal...3763 days ago
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Wire posts
News
IPython: Interactive notebooks
...athematics, plots and rich media into a single document. These notebooks are normal files that can be shared with colleagues, converted to other formats such as HTML or PDF, etc. You...3450 days ago
- ...nters. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allow...
3449 days ago
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Opportunity posts
- ...sirable : Experience in Perl/Python/R Remuneration : Rs. 20,000/- per month (consolidated) Scope of work : 1. Analysis of different file formats and their conversions. 2....
3626 days ago
Bio-Scripts
BioPerl to convert between sequence formats from Fasta to Genbank
#!/usr/local/bin/perl -w # Sequence formats to choose: Fasta, EMBL. GenBank, Swissprot, PIR and GCG use Bio::SeqIO; $inFile = "BRCA2.fa"; $in = Bio::SeqIO->newFh('-file'...2899 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::Es...2899 days ago
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Groups
...dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation o...3886 days ago
Tags
- Reformat is a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (an old Illumina format) bam (if samtools is installed) gzip zip asc...
Tags: Bioinformatics, BBMap/BBTools package, Multipurpose, Tool, Converting, Formats, NGS
2697 days ago
- Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of their respective ends paths, describe genomes,...
Tags: VG, variation, graph, structures, interchange, formats, alignment, genotyping, variant, calling, methods, snp
1543 days ago
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Comments
Comment on "Which of the following programming language is best for a bioinformatics beginner?"
...rl (http://www.bioperl.org/wiki/Main_Page), one of the first biological module repositories that increase the usability from, for example, change formats (Bio::SeqIO) to do phylogenet...3514 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
I love awk but recommend you to try bioawk . Bioawk is a modified version of awk which will parse some common sequence formats. https://github.com/lh3/bioawk3665 days ago
