BOL

The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for...

harvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...

Some five points to keep in mind for bioinformatics software/tools

Bioinformatics tools

1. Ktrim: An extra-fast, accurate adapter trimmer for sequencing data. It processes FASTQ files from multiple lanes with minimal mismatching and over-trimming of adapters.2. BWA MEM: A reliable alignment tool (particularly for mapping ALT contigs...

List of bioinformatics tools/Software Website References for genome assembly:

Frequently used bioinformatics tools for viral genome analysis !

https://gatb.inria.fr/ - The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge...

What are genomic interspersed repeats? In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later...

engr.case.edu - In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological verification of such patterns. Finally we list publicly...