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CBIcall is a workflow-agnostic, configuration-driven framework designed for standardized variant calling in large-scale, federated genomic cohorts.

SMAca: SMA Carrier Analysis tool. SMN1 copy-number and sequence variant analysis from next generation sequencing data. SMAca is a python tool to detect putative SMA carriers and estimate the absolute SMN1 copy-number in a population. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify the so-called “silent carriers” (i.e. individuals with two copies of SMN1 on one chromosome, but none on the other).

Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data. SCSIM: Jointly Simulating Correlated single-cell and bulk next-generation sequencing data. This is a tool for simulating next-generation sequencing data from a hierarchical sampling arrangement with single-cell and bulk samples.

A program for analyzing and selecting sets of barcodes for mgi-sequencing. The application allows analyzing the compatibility of barcodes on a single lane of a flow cell in a set in the case of equal and arbitrary fractions.

Determining the serotype composition of mixed samples of pneumococcus using whole genome sequencing | Pneumococcal serotype quantification using NGS reads | SeroCall can identify and quantitate the capsular serotypes in Illumina whole-genome sequencing samples of S. pneumoniae, calculating abundances of each serotype in mixed cultures. The software is written in Python (compatible with Python 2 or 3), and is freely available under an open source GPLv3 license

ClassifyCNV is a command-line tool that implements the 2019 ACMG guidelines to evaluate the pathogenicity of germline duplications and deletions.

CharPlant (Chromatin Accessible Regions for Plant) is a de novo OCRs prediction tool based on deep learning model. It can take complete DNA sequences or scaffolds as input, and output the outline of OCRs in a .Bed format file rely on sequence features. To our knowledge, this is the first tool to de novo predict potential open chromatin regions from DNA sequence and assay data. The result of OCR (Open Chromatin Region) assay technologies such as DNase-seq and ATAC-seq represents the open state of a tissue at a given time and does not cover all the chromatin accessible information of this species. To predict the potential open regions of different tissues at different times in the whole sequence can help to understand gene transcription and regulation from a global perspective.

Estimation of cell-level SNVs from scRNA-seq data. SCReadCounts is a computational tool for a cell-level assessment of the read counts bearing a particular nucleotide at genomic positions of interest from single cell RNA sequencing (scRNA-seq) data. SCReadCounts is available as a self-contained binary package for 64-bit Linux systems, as Python source, and MacOS (Darwin). The self-contained binary package is appropriate for most Linux and MacOS users. The pythonic version requires pysam, numpy and scipy along with other packages (See the install instructions for more details).

A novel isolation-forest-based package to detect copy number variations from various NGS datasets.