493 Open source projects that are alternatives of or similar to InSilicoSeq

gargammel is an ancient DNA simulator

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

A package for designing compact and comprehensive capture probe sets.

Strain-level abundances estimation in metagenomic samples using variation graphs

Cloud-based single-cell copy-number variation analysis tool

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

General-purpose discrete-event multiagent simulation library for agent-based modelling and simulation

Remove contaminated contigs from genomes using k-mers and taxonomies.

Sequence lineage information extracted from RKI sequence data repo

Finds SNP sites from a multi-FASTA alignment file

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

Meta-Omics Software for Community Analysis

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Maximum likelihood demultiplexing

A low Mach number stellar hydrodynamics code

No description or website provided.

Tools for analyzing 10X Genomics data

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

a julia libarary for simulating the dynamics of ecological communities across space

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Deep learning for Metagenome Assembly Error Detection

UCThello - a board game demonstrator (Othello variant) with computer AI using Monte Carlo Tree Search (MCTS) with UCB (Upper Confidence Bounds) applied to trees (UCT in short)

Fast in-silico normalization algorithm for NGS data

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

HMMRATAC peak caller for ATAC-seq data

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

Simulation of the propagation of incoherent light, aiming to illustrate the concept of spatial coherence.

Framework for Metastatic And Clonal History INtegrative Analysis

Cross platform input simulation in Rust

A curated list of awesome edge computing, including Frameworks, Simulators, Tools, etc.

Improve the quality of a denovo assembly by scaffolding and gap filling

The MG-RAST Backend -- the API server

FASTQ compression

AMBER: Assessment of Metagenome BinnERs

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

AStarix: Fast and Optimal Sequence-to-Graph Aligner

Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

WOSS is a multi-threaded C++ framework that permits the integration of any existing underwater channel simulator that expects environmental data as input and provides as output a channel realization. Currently, WOSS integrates the Bellhop ray-tracing program. Thanks to its automation the user only has to specify the location in the world and the…

Bonsai: Fast, flexible taxonomic analysis and classification

Predict AMPs in (meta)genomes and peptides

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

A visual tool for laying out Gazebo simulation world files.

Collection of scripts for bacterial genomics

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

C++ library for Parsing OpenScenario (1.1.1) & OpenDrive files (1.7) ASAM Specifications

From genomes to phenotypes: Traitar, the microbial trait analyzer

A robust, extensible metagenomics pipeline

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Project for students who want to learn PLC programming but don't have access to real-world machines or constructions to learn programming on.

xHLA: Fast and accurate HLA typing from short read sequence data

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

MaAsLin2: Microbiome Multivariate Association with Linear Models

Conway's Game of Life

Cycle-accurate pre-silicon simulator of RISC-V and MIPS CPUs

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

Experiments with expanded ensembles to explore chemical space

📊复杂网络建模课程设计. The project of modeling of complex networks course.

Data management, integration and modeling with blocks #

Code for quadrotor control