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github.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...

github.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....

github.com - MALVA is able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mapping-free approaches are as accurate as alignment-based ones, while being...

https://arvados.org/ - Arvados is a free and open source bioinformatics platform for genomic and biomedical data. User can Store | Organize | Compute | Share the data for free. 

journals.plos.org - Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for...

userweb.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...

software.broadinstitute.org - Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.Genome STRiP...

ogdraw.mpimp-golm.mpg.de - OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file format, whereas the output format can be chosen among several formats. The...

http://genemania.org/ - Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function...

genome.crg.es - In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by...