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Search results for python sequencing

309 search results found

Deepvariant ⭐ 2,978

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

Nextstrain build for novel coronavirus SARS-CoV-2

Galaxy ⭐ 1,211

Data intensive science for everyone.

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Rna Seq Analysis ⭐ 614

RNAseq analysis notes from Ming Tang

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

Cutadapt ⭐ 475

Cutadapt removes adapter sequences from sequencing reads

Copy number variant detection from targeted DNA sequencing

Sequence correction provided by ONT Research

A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.

Nanoplot ⭐ 336

Plotting scripts for long read sequencing data

Metaphlan ⭐ 242

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

Crispresso2 ⭐ 233

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

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

Sortmerna ⭐ 220

SortMeRNA: next-generation sequence filtering and alignment tool

Cellbender ⭐ 218

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

Circlator ⭐ 193

A tool to circularize genome assemblies

Insilicoseq ⭐ 158

🚀 A sequencing simulator

Afterqc ⭐ 157

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

Readfish ⭐ 152

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Clairvoyante ⭐ 142

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Nanofilt ⭐ 141

Filtering and trimming of long read sequencing data

Antimicrobial Resistance Identification By Assembly

Gubbins ⭐ 133

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

Seq2science ⭐ 132

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Identification of differential RNA modifications from nanopore direct RNA sequencing

Rnalysis ⭐ 114

RNA sequencing analysis software

Crispresso ⭐ 110

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

Deepbinner ⭐ 108

a signal-level demultiplexer for Oxford Nanopore reads

Ngscheckmate ⭐ 106

Software program for checking sample matching for NGS data

Optitype ⭐ 106

Precision HLA typing from next-generation sequencing data

Accurate and flexible loops calling tool for 3D genomic data.

A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

Rna Seq Pipeline ⭐ 88

Ngs Pipe ⭐ 87

NGS-pipe: next-generation sequencing pipelines for precision oncology

Hybpiper ⭐ 83

Recovering genes from targeted sequence capture data

Parliament2 ⭐ 83

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Kneaddata ⭐ 78

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

Nanocaller ⭐ 78

Variant calling tool for long-read sequencing data

Nanopype ⭐ 78

Snakemake pipelines for nanopore sequencing data archiving and processing

Phylowgs ⭐ 78

Application for inferring subclonal composition and evolution from whole-genome sequencing data.

Neat Genreads ⭐ 72

NEAT read simulation tools

Deepnovo ⭐ 67

Protein Identification with Deep Learning

GolfDB: A Video Database for Golf Swing Sequencing

A package for designing compact and comprehensive capture probe sets.

SV caller for nanopore data

Nanostat ⭐ 63

Create statistic summary of an Oxford Nanopore read dataset

Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.

Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.

Nanocompore ⭐ 56

RNA modifications detection from Nanopore dRNA-Seq data

Pyflow Chipseq ⭐ 55

a snakemake pipeline to process ChIP-seq files from GEO or in-house

Method for detecting STR expansions from short-read sequencing data

Screenprocessing ⭐ 51

Atac Seq ⭐ 51

Poreplex ⭐ 51

A versatile sequenced read processor for nanopore direct RNA sequencing

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

Pipeline for processing inDrops sequencing data

Svim Asm ⭐ 48

Structural Variant Identification Method using Genome Assemblies

MARVEL: Metagenomic Analyses and Retrieval of Viral ELements

Pipeline Standardization ⭐ 47

Python3 scripts to manipulate FASTA and FASTQ files

Grabseqs ⭐ 44

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Ncov Tools ⭐ 44

Small collection of tools for performing quality control on coronavirus sequencing data and genomes

Genome guided re-segmention and visualization for raw nanopore sequencing data.

BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis

Bsseeker2 ⭐ 42

A versatile aligning pipeline for bisulfite sequencing data

Ngspeciesid ⭐ 41

Reference-free clustering and consensus forming of long-read amplicon sequencing

Viral infection diagnostics using next-generation sequencing

Hic_pipeline ⭐ 40

An easy-to-use Hi-C data processing software supporting distributed computation.

Sequencing ⭐ 39

A flexible and simple framework for sequence to sequence learning.

vahatraker - a live midi sequencer/tracker for JACK/GTK

de novo virus assembler of Illumina paired reads

Mapdamage ⭐ 37

mapDamage: tracking and quantifying damage patterns in ancient DNA sequences

Dadasnake ⭐ 37

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake

Ngstools ⭐ 37

Next-Generation Sequencing(NGS) toolkits.

Read_until_api ⭐ 36

Read Until client library for Nanopore Sequencing

Data_science_in_biology ⭐ 35

projects using galaxy, python, linux command line to analyze sequencing data

Mgefinder ⭐ 35

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

Structural variant caller for low-depth long-read sequencing data

Biocommons.seqrepo ⭐ 34

non-redundant, compressed, journalled, file-based storage for biological sequences

Airr Standards ⭐ 34

AIRR Community Data Standards

Graph-based assembly phasing

Covid 19 Signal ⭐ 32

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

Module for reading ABI Sanger sequencing trace files

Mitofinder ⭐ 32

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

Fast and accurate tool for estimating genomic distances between genome-skims

EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

Nano Snakemake ⭐ 31

A snakemake pipeline for SV analysis from nanopore genome sequencing

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.

A Python package for microbiome sequencing analysis with QIIME 2

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

High throughput sequencing analysis tools

Amplicon_sequencing_pipeline ⭐ 30

Pipeline for computing OTU tables from 16S or ITS amplicon sequencing data.

Next-Gen Sequencing tools from the Horvath Lab

The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline

Treetoreads ⭐ 29

Pipeline to generate NGS reads from a phylogeny

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

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