github.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of:
nodes, which are labeled by sequences and ids
edges, which connect two nodes via either of...
genome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data.
https://genome.sph.umich.edu/wiki/Vt
https://github.com/atks/vt
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...
github.com - Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only
Cycles enumeration (aka Bubbles) as part of de novo de bruijn...
bioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...
github.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...
jimb.stanford.edu - The Genome in a Bottle (GIAB) Consortium is a public-private-academic consortium hosted by NIST to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of whole human genome...
github.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...
github.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...
github.com - GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general,...