Next Generation Sequencing (NGS)
Rahul Agarwal 4616 days ago
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List of popular bioinformatics software/tools
By Jitendra Narayan 4617 days ago Comments (28)samtools.sourceforge.net - 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.mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 2305 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...Picard
By Neel 3599 days agobroadinstitute.github.io - 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...
sam to bam conversion !!
Last updated 2962 days ago by JitTo 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...Fancy Oneliner for Bioinformatics !!
By Poonam Mahapatra 3530 days agouserweb.eng.gla.ac.uk - 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...Qualimap2: Evaluating next generation sequencing alignment data
By Jit 2734 days agoqualimap.bioinfo.cipf.es - Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like...bedtools
By Jit 3298 days agobedtools.readthedocs.io - 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...Quip: Aggressive compression of FASTQ, SAM and BAM files.
By Neel 1383 days agogithub.com - This will help us to reduce the amount of drive space we take up and decrease data transfer times Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in...BBTools for bioinformatician !
By Surabhi Chaudhary 2941 days ago Comments (1)BBTools can do almost everything now !
