284 Open source projects that are alternatives of or similar to CAMSA

Suite of tools for use in genome assembly and consensus. Work in progress.

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

find large indels (in the blind spot between GATK/freebayes and SV callers)

A fast tool for hybrid genome assembly of long and short reads

Large genome reassembly based on Hi-C data, continuation of GRAAL

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

De novo genome assembly and multisample variant calling

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

An interactive web portal for exploring immuno-oncology data

Bystro genetic analysis (annotation, filtering, statistics)

Fast alignment and preprocessing of chromatin profiles

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Version 2.1.0 released

Toolkit for preparing genomes for submission to NCBI

The Ensembl Compara Perl API and SQL schema

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

A simple command-line tool to download data from Joint Genome Institute databases

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

An ontology of cell types

Assembling the cause of phenotypes and genotypes from NGS data

(WIP) best-practices workflow for rare disease

A modular annotation tool for genomic variants

pythonic wrapper for htslib

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Feature Annotation Location Description Ontology

PERF is an Exhaustive Repeat Finder

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Home of the Genomic Feature and Variation Ontology (GFVO)

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

A faster lmm for GWAS. Supports GPU backend.

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

My collection of light bioinformatics analysis pipelines for specific tasks

Compute N50/NG50 and auN/auNG

Chanjo provides a better way to analyze coverage data in clinical sequencing.

Inference of switch-like differential expression along single-cell trajectories

Environmental DNA metabarcoding taxonomic identification

A package for designing compact and comprehensive capture probe sets.

Provide R access to the NCI Genomic Data Commons portal.

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Complex structural variant detection from WGS data

Close assembly gaps using long-reads at high accuracy.

Clustering scRNAseq by genotypes

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

A proof of concept of RNAseq pipeline

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

Introduction to Cloud Computing for Genomics

An open-access bioinformatics text

Fast hash function for DNA sequences

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

echt rapid variant annotation and filtering

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Learn interpretable computational phenotyping models from k-merized genomic data