Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1761 days ago
Cactus: a reference-free whole-genome multiple alignment program
Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here:&...oximately 120 CPU-days of compute per genome, with about 120 GB of RAM used at peak. T...1744 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sed...s less than a minute and the whole pipeline with SV calling takes ~2 minutes. Intact ord...embly correction GFF lift-over Structural variant calling with and integrated version o...1668 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minu...30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a B...1647 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly accou...1615 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 written in C and runs in Linux. FastGT uses a list...1575 days ago
1575 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 201...o 03/19/15 Introduction to variant discovery: calling cohorts Louis Bergelson PDF Video 03/19/15 Variant calling and joint genotyping Sheila...1550 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the ta...porary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs ag...1464 days ago
URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA...e accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage...1299 days ago