Nanopolis: polish a genome assembly
...ford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a...2133 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (in...phylogenomic tree). snippy --cpus 16 --outdir mysnps --ref Listeria.gbk --R1 FDA_R...2048 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
...sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacem...2042 days ago
geck: trio-based comparative benchmarking of variant calls
Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenazim trio and t...1835 days ago
FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies
...he SNP2GENE function takes GWAS summary statistics as an input, and provides extensive functional annotation for all SNPs in genomic areas identified by lead SNPs. The GENE2FUNC ...1823 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
...active, configurable and elegant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like genes,SNPs etc.) on the chromosome plot....1725 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...ution is to search the graph in multicores shared memory parallel mode using graph decomposition then use filtering method to generate good quality SNPs. https://arxiv.org/abs/1809....1582 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 Mapping-free appro...1582 days ago
mutatrix: a population genome simulator which generates simulated genomes.
genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms More at https://github.com/ekg/mutatrix ./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta1582 days ago
1550 days ago