Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves bot...2016 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVAT...et/projects/excavatortool/.EXCAVATOR is a novel software package for the detection of copy number variants (CNVs...1945 days ago
1928 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA&n...1928 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
...sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred...1865 days ago
MFannot : a program for the annotation of mitochondrial and plastid genomes
...mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools. It makes intense use of RNA/intron detection tools including HMMER,&n...1711 days ago
ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have...1568 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...1557 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.1536 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA&n...1514 days ago