BOL: Related items

List of popular bioinformatics software/tools

Jitendra Narayan — Tue, 16 Jul 2013 14:30:30 -0500

In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.

Address of the bookmark: http://samtools.sourceforge.net/swlist.shtml

Structure of Binary files used for storing sequencing data-bam and sff

Rahul Agarwal — Sun, 11 Aug 2013 14:29:49 -0500

Many times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less space in memory with maximum information content.

Link for those who looking for structure of Bam and sff file:

Bam:

http://samtools.sourceforge.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

Binary file Editor and Viewer:

http://mh-nexus.de/en/hxd/

SCALCE

Surabhi Chaudhary — Fri, 15 Apr 2016 05:09:51 -0500

SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any valid FASTQ with consistent read lengths.

More at http://sfu-compbio.github.io/scalce/

Address of the bookmark: http://sfu-compbio.github.io/scalce/

Picard

Neel — Fri, 29 Apr 2016 08:21:54 -0500

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.

Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub.

The Picard toolkit is open-source under the MIT license and free for all uses.

Enjoy!

Address of the bookmark: http://broadinstitute.github.io/picard/

sam to bam conversion !!

Jit — Fri, 26 Jan 2018 02:36:18 -0600

To do sam to bam conversion, follow the following commands :-

Code:

$ samtools view -b -S file.sam > file.bam

Then you will need to use

Code:

$ samtools sort file.bam file-sorted

followed by

Code:

$ samtools index  file-sorted.bam

in order to get an indexed file.

If you just type

Code:

$ samtools

or samtools followed by the name of one of the samtools commands, you will get a few lines of help giving the correct syntax for that command,

Fancy Oneliner for Bioinformatics !!

Poonam Mahapatra — Thu, 07 Jul 2016 12:05:50 -0500

This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are sharing these codes with the intention that if they are useful and help you in your analyses, then we will be appropriately credited as considerable effort has been put into devising them.

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html

vcfR: a package to manipulate and visualize VCF data in R

Jit — Thu, 25 Oct 2018 09:05:59 -0500

VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file or converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and the R environment connecting familiar software with genomic data.

Address of the bookmark: https://github.com/knausb/vcfR

Fastq stats in Emoji :)

Rahul Nayak — Mon, 06 Aug 2018 10:20:20 -0500

Read one or more FASTQ files, fastqe will compute quality stats for each file and print those stats as emoji... for some reason.

Given a fastq file in Illumina 1.8+/Sanger format, calculate the mean (rounded) score for each position and print a corresponding emoji!

https://fastqe.com/

Address of the bookmark: https://github.com/lonsbio/fastqe

bedtools

Jit — Fri, 24 Feb 2017 04:50:44 -0600

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one tointersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.

Address of the bookmark: http://bedtools.readthedocs.io/en/latest/index.html

BamView: a free interactive display of read alignments in BAM data files

Neel — Fri, 09 Nov 2018 13:43:22 -0600

To run the application on UNIX from the downloaded jar file run the UNIX:

java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

Address of the bookmark: http://bamview.sourceforge.net/