363 Open source projects that are alternatives of or similar to mapping-iterative-assembler

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

A fast whole-genome aligner based on de Bruijn graphs

SDK for GPU accelerated genome assembly and analysis

Genomics Workflows on AWS

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

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

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

Finds SNP sites from a multi-FASTA alignment file

A custom layout object based on flow layout. Added supports for horizontal, vertical alignment and RTL direction of collection view items.(available for both UICollectionView and NSCollectionView)

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

Easy genetic ancestry predictions in Python

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

Population assignment analysis using R

GA4GH Variation Representation Python Implementation

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

uLTRA is a long-read splice aligner with high accuracy from using a guiding annotation

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

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

Seven Bridges Genomics aligner/caller debugging and analysis tools

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

Displayed width of UTF-8 strings in Modern C++

A WGS de novo assembler based on the FMD-index for large genomes

Genome Annotation Without Nightmares

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

Haplotype VCF comparison tools

Genome-wide imputation pipeline

DriverPower

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

simple viewer for variant call format using htslib

Python package and CLI for whole-genome duplication related analyses

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Deep neural network for the alignment of GC-MS peaks

Find target sites for the miRNAs in genomic sequences

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

A secure encryption tool for genomic data

Phage-Host Interaction Search Tool

Official git repository for Biopython (originally converted from CVS)

A python and C++ library for reading and writing neuronal morphologies

a pileup library that embraces the huge

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

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Collection of scripts for bacterial genomics

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

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

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

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Python package for extracting and analyzing image representations from state-of-the-art neural networks for computer vision

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

A DNA Sequence Alignment/Map (SAM) library for Clojure

Biopython Jupyter Notebook tutorial to characterize a small genome

JavaScript VisualizationTools

use the noise

cython + htslib == fast VCF and BCF processing

simuG: a general-purpose genome simulator

Needleman-Wunsch and Smith-Waterman algorithms in python

ntHash implementation in Rust

Facial Landmark Detection based on PyTorch