BOL

LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA...

Comparative Genomics Study of #Multi-Drug-Resistance #Mechanisms in the #Antibiotic-Resistant Streptococcus suis R61 Strain https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180280/

Interesting plotting https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0678-1 #Plot #Structure #Variation #Cotton

This research paper is also useful http://www.sciencedirect.com/science/article/pii/S1046202316300184

quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve...

MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs) Description MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any...

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the...

NGS tutorial http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html #NGS #Tutorial #Example

GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two...

The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux...

Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on...

RA Bioinformatics at NBAIR http://www.nbair.res.in/employment/RA&YP.pdf #Bioinformatics #RA #Jobs #NBAIR

Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools...

R package to Finds Synteny in a Sequence Database http://origin.rdrr.io/bioc/DECIPHER/man/FindSynteny.html

Synteny database https://ecrbase.dcode.org/synteny.php #Synteny #Database

General concepts: concurrency, #parallelism, #threads and #processes http://learn-gevent-socketio.readthedocs.io/en/latest/general_concepts.html

Accept file from STDIN in Perl my $infh = \*STDIN; my $outfh = \*STDOUT #Perl #Tricks

You can also try LAZER, it produces the same evaluation as Quast but is 5.6 times faster and use half the memory http://www.csd.uwo.ca/~ilie/LASER/

E-MEM is a C++/OpenMP program designed to efficiently compute MEMs between large genomes. See the README file for instructions on how to use E-MEM. E-MEM source code The source code can be downloaded here. If you use E-MEM, please...