jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina...ce genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant...1744 days ago
1687 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes. Intact ord...nting of contigs. Misassembly correction GFF lift-over Structural variant calling with and integrated version o...1651 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 minutes...30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a B...1630 days ago
HaploTypo: a variant-calling pipeline for phased genomes
...d haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly accou...HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference...1598 days ago
GfaViz: flexible and interactive visualization of GFA sequence graphs
GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was o...rent types of sequence graphs, including scaffolding graphs, alignment graphs, variant...1563 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 reference genom...ndance based method calls single nucleotide variants (SNVs), multinucleotide vari.../deletion variants (indels), and structural variant...1558 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 of variant...1558 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/vt1558 days ago
1558 days ago