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Search results for python ngs
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131 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.
Galaxy
⭐
1,211
Data intensive science for everyone.
Deeptools
⭐
644
Tools to process and analyze deep sequencing data.
Snakepipes
⭐
359
Customizable workflows based on snakemake and python for the analysis of NGS data
Bioconvert
⭐
344
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Python Musicbrainzngs
⭐
222
Python bindings for Musicbrainz' NGS webservice
Sortmerna
⭐
220
SortMeRNA: next-generation sequence filtering and alignment tool
Afterqc
⭐
157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
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.
Viral Ngs
⭐
129
Viral genomics analysis pipelines
Atropos
⭐
116
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
Crispresso
⭐
110
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
Ngscheckmate
⭐
106
Software program for checking sample matching for NGS data
Cloops
⭐
99
Accurate and flexible loops calling tool for 3D genomic data.
Isoquant
⭐
98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Reg Gen
⭐
96
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Platon
⭐
93
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Tadbit
⭐
89
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
Ngs Pipe
⭐
87
NGS-pipe: next-generation sequencing pipelines for precision oncology
Bamnostic
⭐
84
a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool
Recentrifuge
⭐
83
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Mcclintock
⭐
83
Meta-pipeline to identify transposable element insertions using next generation sequencing data
Tbprofiler
⭐
81
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
Spark
⭐
81
Publication quality NGS track plotting
Genomics
⭐
78
Scripts, utilities and programs for genomic bioinformatics.
Catch
⭐
63
A package for designing compact and comprehensive capture probe sets.
Iskylims
⭐
61
is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
Fastq And Furious
⭐
49
Efficient handling of FASTQ files from Python
Grabseqs
⭐
44
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
Pipeliner
⭐
44
An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
Cfdnapattern
⭐
42
Pattern Recognition for Cell-free DNA
Ngs Primerplex
⭐
42
NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design
Circle Map
⭐
39
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
Pcangsd
⭐
38
Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
Mapdamage
⭐
37
mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
Ngstools
⭐
37
Next-Generation Sequencing(NGS) toolkits.
Oxbow
⭐
32
Read specialized NGS formats as data frames in R, Python, and more.
Ngs_pipeline
⭐
31
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Pygtftk
⭐
30
A python package and a set of shell commands to handle GTF files
Vapid
⭐
27
VAPiD: Viral Annotation and Identification Pipeline
Demultiplex
⭐
26
Versatile FASTA/FASTQ demultiplexer.
Atacseq_pipeline
⭐
25
Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.
Insaflu
⭐
24
INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance
Cris.py
⭐
24
Analyze NGS data for CRISPR (or any engineered endonuclease) activity and screen for clones. Screen for NHEJ or multiple HDR events concurrently.
Ngstools
⭐
23
My own tools code for NGS data analysis (Next Generation Sequencing)
Pathogentrack
⭐
22
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
Pm4ngs
⭐
21
Project Manager for NGS data analysis
Kgwasflow
⭐
19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Seqqscorer
⭐
18
Rnaseq Pipeline
⭐
18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Looper
⭐
18
A job submitter for Portable Encapsulated Projects
Symportal_framework
⭐
18
SymPortal is an analytical tool used to identify Symbiodiniaceae genotypes using Illumina rDNA ITS2 amplicon NGS data.
Open_pipelines
⭐
17
Pipelines for NGS data preprocessing by the Bock lab and friends
Icallsv
⭐
16
A Framework to call Structural Variants from NGS based datasets
Mgse
⭐
16
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
S4 Clarity Lib
⭐
16
A modern Python library for BaseSpace Clarity LIMS.
Myvcf
⭐
16
myVCF: a web-based platform for target and exome mutations data management
Echoprint Albumidentify
⭐
15
Experimenting with echoprint and musicbrainz
Daylily
⭐
15
A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.
Manorm
⭐
14
A robust model for quantitative comparison of ChIP-Seq data sets.
Scripts
⭐
14
Scripts to handle NGS data and other biological data
Ngs Test Data
⭐
14
A workflow for creating small NGS test data sets, useful for continuous integration.
Indextools
⭐
14
IndexTools is a toolkit for extremely fast NGS analysis based on index files.
Pybioviz
⭐
14
bioinformatics visualization tools with pyviz/bokeh
Seroba
⭐
14
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Ampliconreconstructorom
⭐
14
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
Rnftools
⭐
13
RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
Seqflow
⭐
13
My pipeline and code collections for NGS data analysis, such as RNA-seq, ChIP-seq, MNase-seq, Hi-C, Trac-looping and etc, mainly keep the analysis within Python.
Chronqc
⭐
13
Manuscript describing ChronQC is now available online in Bioinformatics
Toolkit
⭐
13
A toolkit for NGS analysis with Python
Spp Idr
⭐
12
Wrappers around NGS peak callers to both call peaks and run IDR
Jovian
⭐
12
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.
Ngs Pipeline
⭐
12
Pipeline for Somatic Variant Calling with WES and WGS data
Cava
⭐
12
CAVA (Clinical Annotation of VAriants)
Mix
⭐
11
MIX: Combining multiple assemblies from NGS data
Samsift
⭐
11
SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.
Locings
⭐
10
Code for my Summer of Code Project, "loci-NGS", which is a program for manipulating, storing and outputting large multi-locus datasets.
Abtools
⭐
10
Analysis of antibody NGS data
Assnake
⭐
10
Snakemake based framework for NGS data analysis and management
Workflows
⭐
10
snakemake-based workflows
Monsda
⭐
10
MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis
Ngsderive
⭐
10
Forensic analysis tool useful in backwards computing information from next-generation sequencing data.
Banzai Microbialgenomics Pipeline
⭐
10
Banzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool developed within Dr Scott Beatson’s Group at the University of Queensland
4pipe4
⭐
10
A NGS data analysis pipeline with emphasis on SNP detection
Fastqwiper
⭐
9
An ensamble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and fix reads interleaving.
Tophat Recondition
⭐
9
Post-processor for TopHat unmapped.bam files making them useable by downstream software.
Iseq
⭐
9
An integrated analysis toolkit and pipeline for Next-Generation Sequencing (NGS) panel sequencing data
Pythonngstools
⭐
9
Scripts for NGS processing
Variantconvert
⭐
9
A customizable genetic variants file format converter.
Genedock
⭐
9
About Genedock
Star Seqr
⭐
9
RNA Fusion Detection and Quantification
Ansible Pipelines
⭐
8
Negspy
⭐
8
Python NGS Repository
Nanosim H
⭐
8
NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.
Viral Assemble
⭐
8
viral-ngs: genome assembly and scaffolding
Ngs Pipeline
⭐
8
All kinds of NGS analysis pipeline
Ngs Workflows
⭐
8
Source code, data and documentation to demonstrate automation in NGS data analysis
Xenomapper
⭐
8
A utility for splitting mixed origin NGS reads
Captus
⭐
8
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
Auto_process_ngs
⭐
8
Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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