Structure of Binary files used for storing sequencing data-bam and sff
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 fo...3882 days ago
Most Commonly used Awk by Bioinformatician
...lace a pipeline of 'stuff | grep | sed | cut...' with a single call to awk. For a simple script, most of the timelag is in loading these apps into memory, and it's much faster to do i...3875 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...han 6 days using 54 Gb of RAM and a 123-processor compute cluster for calculation of an FM-index of the 1.2 billion reads] Readjoiner: a fast and memory efficient string graph-based...3742 days ago
Next generation sequencing in R or bioconductor environment
...strings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It contains many speed and memory effective string containers,...3587 days ago
Commercial and public next-gen-seq (NGS) software
...Homer, Stanley F. Nelson and Barry Merriman at UCLA.Bowtie - Ultrafast, memory-efficient short read aligner....25 million reads per hour on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Trans...3481 days ago
Software packages for next gen sequence analysis
...Barry Merriman at UCLA. * Bowtie - Ultrafast, memory-efficient short read aligner....r on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Trans...to reference genome assemblies; in a fast and memory-efficient manner. Robust to I...3205 days ago
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Genome Assembly Tools and Software - PART1 !!
...For the sake of computational memory saving and convenience of dat...g Gapless Reads A fast and memory-efficient method for haplotyp...is both multi-core aware and memory efficient, allowing it to han...ortex is an efficient and low-memory software framework for analys...2648 days ago