211 Open source projects that are alternatives of or similar to indigo

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

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

In-silico PCR and variant primer design

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.

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

parallelized blat with multi-threads support

PEPPER-Margin-DeepVariant

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

Fast and accurate sequence demultiplexing

Polyrhythmic Sequencer library for Web Audio API.

Double Sided Assembly Line Balancing with Genetic Algorithm (C#)

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Antimicrobial Resistance Identification By Assembly

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Rapid large-scale prokaryote pan genome analysis

An interactive web tool for quality control of DNA sequencing data

Assembling the cause of phenotypes and genotypes from NGS data

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

🚀 A sequencing simulator

Intuitive local web frontend for the BLAST bioinformatics tool

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

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

AStarix: Fast and Optimal Sequence-to-Graph Aligner

Sequence lineage information extracted from RKI sequence data repo

Official code repository for GATK versions 4 and up

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

Simple & Efficient data access for Scala and Scala.js

A collection of scripts and notes related to genomics and bioinformatics

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Analysis Pipeline for Single Cell ATAC-seq

RNASeq pipeline

Genomics Extension for SQLite

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

Structural variant toolkit for VCFs

Multilocus sequence typing by blast using the schemes from PubMLST

A package for designing compact and comprehensive capture probe sets.

A repository for setting up a RNAseq workflow

Discovering known and novel miRNAs from small RNA sequencing data

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

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

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

A Java API for high-throughput sequencing data (HTS) formats.

Tools for analyzing 10X Genomics data

Analysis pipelines for sequencing data

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

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Framework for Metastatic And Clonal History INtegrative Analysis

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

gargammel is an ancient DNA simulator

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

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

A collection of publications on comparison of high-throughput sequencing technologies.

Maximum likelihood demultiplexing

FASTQ compression

A tool to circularize genome assemblies

A python-based isomiR quantification and analysis pipeline

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

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