GATK HaplotypeCaller

liftOver — UCSC genome coordinate conversion tool for remapping genomic intervals between genome assemblies (e.g., hg19 to hg38, mm10 to mm39). Converts BED, GFF, GTF, VCF, and positional data across

1 shared topic • 3 shared operations

medaka -- neural network-based tool from Oxford Nanopore Technologies for creating consensus sequences and calling variants from nanopore sequencing data. Polishes draft assemblies from Flye, miniasm,

1 shared topic • 3 shared operations

Use when working with minipolish — Racon-based polishing of miniasm long-read genome assemblies. Accepts raw nanopore or PacBio reads (FASTQ/FASTA) and a miniasm GFA assembly, runs iterative minimap2

1 shared topic • 3 shared operations

Pilon — automated genome assembly improvement and variant detection tool. Polishes draft assemblies by correcting SNPs, indels, and misassemblies using short-read alignments (BAM files). Fills gaps in

1 shared topic • 3 shared operations

SvABA -- structural variant and indel caller using genome-wide local assembly. Detects deletions, insertions, duplications, inversions, and complex rearrangements from short-read (Illumina) whole-geno

1 shared topic • 3 shared operations