170 Open source projects that are alternatives of or similar to ilus

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

C library for high-throughput sequencing data formats

Whole Exome/Whole Genome Sequencing alignment pipeline

Sentieon DNAseq

Method to optimally select samples for validation and resequencing

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

Learning the Variant Call Format

Spark VCF data source implementation for Dataframes

My bioinfo toolbox

simple viewer for variant call format using htslib

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

GREIN : GEO RNA-seq Experiments Interactive Navigator

No description or website provided.

Powerful statistics for VCF files

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

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

Population-wide Deletion Calling

An automated RNA-seq pipeline using Nextflow

myVCF: a web-based platform for target and exome mutations data management

Collection of scripts for bacterial genomics

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

Python toolkit for building restartable pipelines

calcardbackup: moved to https://codeberg.org/BernieO/calcardbackup

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.

Multi-sample somatic variant caller

🐳 Bio-dockers: dockerized bioinformatic tools

Ultrafast sequence typing and gene detection from NGS raw reads

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

💾 📃 "Reads to report" for public health and clinical microbiology

A bioinformatics pipeline to analyze mtDNA from NGS data

📊Evaluating, filtering, comparing, and visualising VCF

Cancer Predisposition Sequencing Reporter (CPSR)

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Detect novel (and reference) STR expansions from short-read data

Fast and accurate gene fusion detection from RNA-Seq data

Faster BWA-MEM2 using learned-index

PEPPER-Margin-DeepVariant

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Bioinformatics curated workflows that use Biocontainers tools

Finds SNP sites from a multi-FASTA alignment file

Utilities for analyzing next generation sequencing data.

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

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

A library for manipulating bioinformatics sequencing formats in Apache Spark

An easy-to-use way for running Galaxy workflows.

<<------ Use SnapATAC!!

A workflow for creating small NGS test data sets, useful for continuous integration.

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

Distribution of TEs and their relationship to genes in host genome

A tool for fast and accurate summarizing of variant calling format (VCF) files

A fluent builder class for vCard files.

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

Efficient handling of FASTQ files from Python