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123 search results found

Cs Video Courses ⭐ 62,887

List of Computer Science courses with video lectures.

Minimap2 ⭐ 1,613

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Seqtk ⭐ 1,148

Toolkit for processing sequences in FASTA/Q formats

Foldseek ⭐ 545

Foldseek enables fast and sensitive comparisons of large structure sets.

BWK awk modified for biological data

Hh Suite ⭐ 429

Remote protein homology detection suite.

Minigraph ⭐ 367

Proof-of-concept seq-to-graph mapper and graph generator

Genometools ⭐ 261

GenomeTools genome analysis system.

🔬 BEDOPS: high-performance genomic feature operations

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Miniprot ⭐ 231

Align proteins to genomes with splicing and frameshift

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Mrbayes ⭐ 201

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

minepy - Maximal Information-based Nonparametric Exploration

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

UCSC Genome Browser source tree. Stable branch: "beta".

Reads simulator

Gfatools ⭐ 181

Tools for manipulating sequence graphs in the GFA and rGFA formats

Biowasm ⭐ 165

WebAssembly modules for genomics

Bio Playground ⭐ 146

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

Cgranges ⭐ 144

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Metaeuk ⭐ 142

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

Biofast ⭐ 132

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Mutscan ⭐ 127

Detect and visualize target mutations by scanning FastQ files directly

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Global alignment and alignment extension

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Fast multi-line FASTA/Q reader in several programming languages

A fast multiple sequence alignment program.

Fqtools ⭐ 105

An efficient FASTQ manipulation suite

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

Pangene ⭐ 100

WIP: Constructing a pangenome gene graph

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

Freesasa ⭐ 95

C-library for calculating Solvent Accessible Surface Areas

Genefuse ⭐ 86

Gene fusion detection and visualization

Mccortex ⭐ 86

De novo genome assembly and multisample variant calling

Yet another k-mer analyzer

Flexible genotype query among 30,000+ samples whole-genome

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

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

Fermi Lite ⭐ 67

Standalone C library for assembling Illumina short reads in small regions

Libbigwig ⭐ 62

A C library for handling bigWig files

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

📇 Retrieve data in genomic intervals with a Python interface for tabix.

Model and predict short DNA sequence features with neural networks

Protein Alignment and Detection Interface

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

Bio Pipeline ⭐ 45

My collection of light bioinformatics analysis pipelines for specific tasks

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

Software for biomolecular electrostatics and solvation calculations

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI

10x Genomics Reads Simulator

A reimplementation of the WaveFront Alignment algorithm at low memory

♥ Efficient Estimation of Evolutionary Distances

Uniquekmer ⭐ 33

Generate unique KMERs for every contig in a FASTA file

Lordfast ⭐ 31

Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

Exact Tandem Repeat Finder (not a TRF replacement)

Spacepharer ⭐ 28

SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

Soapdenovo Trans ⭐ 27

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.

Introduction to Programming for Bioinformatics, based on previous GNBF5010 Introduction to Programming course in Chinese University of Hong Kong

Small general purpose library for C and Python with focus on bioinformatics.

Evaluating genome assemblies

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)

Avxwindowfmindex ⭐ 24

A fast, AVX2 and ARM Neon accelerated FM index library

Soap3 Dp ⭐ 24

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.

GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment

Python bindings to UCSC BigWig and BigBed library

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39

An experimental tool to estimate the similarity between all pairs of contigs

Cgpbigwig ⭐ 22

BigWig manpulation tools using libBigWig and htslib

Scaff10x ⭐ 20

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

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.

♥ Essential Functions for DNA Manipulation

Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.

R Interface to CoreArray Genomic Data Structure (GDS) Files (Development version only)

Find target sites for the miRNAs in genomic sequences

Symmetric DUST for finding low-complexity regions in DNA sequences

bioGUI provides install modules for bioinformatic software for users and allows developers to script a GUI for their applications.

Catsequences ⭐ 15

A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses

Mapping Iterative Assembler ⭐ 15

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

A python library for accessing 2bit files

Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux. These libraries provide usefull utilities for bioinformatics programming in C. This may contain some of my own libraries for bioinformatics utilities as well as long as they install easily on both my mac and linux box.

LAVA: Lightweight Assignment of Variant Alleles

Secphase ⭐ 12

Phasing reads with secondary alignments

Indelpost ⭐ 11

Python library for simple and complex indels.

Libflagstats ⭐ 11

Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.

Better Alignments with Translated HMMER

Alignment-free simulation, computation, and visualization of Low-compexity regions in biological data

Ssw_aligner ⭐ 10

Python implementation of Striped Smith-Waterman Algorithm

bgzf/ciso/daxcr/dictzip/gzinga/migz/razf frontends using zlib/zlib-ng/7-zip/zopfli/libdeflate/miniz/libslz/ backends with parallel (de)compression. compilable with gcc/clang/icc/open64.

A Pedantic FASTA Parser and Tool Set

Genextender ⭐ 8

R/Bioconductor package for optimized functional annotation of ChIP-seq data

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

Biobench2 ⭐ 8

Bioinformatics benchmarking package, based on the original BioBench developed by Albayraktaroglu et al, 2005

Clann: constructing consensus trees and supertrees from multiple source trees

A suite of tools to build and search generalized profiles

genotyping by Mapping-free ALternate-allele detection of known VAriants

Mrna_vaccine_badge ⭐ 7

A small badge showing a schematic of an mRNA vaccine nanoparticle and blinking the RNA sequence of the Moderna or Pfizer vaccines.

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