1588 days ago
StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into...o assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its inpu...1418 days ago
1554 days ago
Kevler: Reference-free variant discovery in large eukaryotic genomes
Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a re...based method calls single nucleotide variants (SNVs), multinucleotide varia...on variants (indels), and structural variants (SVs) simultaneously with a s...1551 days ago
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is...1551 days ago
MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants
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 Mappi...1551 days ago
vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
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/vt1551 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and...f ~/human_g1k_v37.fasta -t 20:62900077-62902077 -v variants.vcf.gz \ -s AAATGTAAACA...1551 days ago
SeqMule: Automated human exome/genome variants detection
SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.1530 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of th...bration Bertrand Haas PDF Video 03/19/15 Introduction to working with variants Yossi Farjoun PDF Video...1526 days ago