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sequencing
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1,038 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.
Fastp
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1,602
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.
Gatk
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1,576
Official code repository for GATK versions 4 and up
Samtools
⭐
1,496
Tools (written in C using htslib) for manipulating next-generation sequencing data
Ncov
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1,348
Nextstrain build for novel coronavirus SARS-CoV-2
Galaxy
⭐
1,211
Data intensive science for everyone.
Getting Started With Genomics Tools And Resources
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991
Unix, R and python tools for genomics and data science
Adam
⭐
966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Picard
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914
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Rnaseq
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718
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Mosdepth
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617
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Rna Seq Analysis
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614
RNAseq analysis notes from Ming Tang
Scrnaseq Analysis Notes
⭐
540
scRNAseq analysis notes from Ming Tang
Phyloseq
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520
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
Uncalled
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507
Raw nanopore signal mapper that enables real-time targeted sequencing
Fetch
⭐
494
Simple & Efficient data access for Scala and Scala.js
Sniffles
⭐
479
Structural variation caller using third generation sequencing
Cutadapt
⭐
475
Cutadapt removes adapter sequences from sequencing reads
Cnvkit
⭐
435
Copy number variant detection from targeted DNA sequencing
Fastqc
⭐
362
A quality control analysis tool for high throughput sequencing data
Medaka
⭐
359
Sequence correction provided by ONT Research
Isobar
⭐
348
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.
Hisat2
⭐
345
Graph-based alignment (Hierarchical Graph FM index)
Nanoplot
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336
Plotting scripts for long read sequencing data
Manta
⭐
333
Structural variant and indel caller for mapped sequencing data
Sars Cov 2_sequencing
⭐
333
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
Elm D3
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328
Elm bindings for D3.js
Sarek
⭐
299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Fgbio
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292
Tools for working with genomic and high throughput sequencing data.
Mixcr
⭐
291
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
Truvari
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284
Structural variant toolkit for VCFs
Htsjdk
⭐
271
A Java API for high-throughput sequencing data (HTS) formats.
Snap
⭐
269
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
Shasta
⭐
269
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
Sequenceserver
⭐
259
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
Mercury
⭐
255
A minimal and human-readable language and environment for the live coding of algorithmic electronic music.
Metaphlan
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242
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Comp Genomics Class
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236
Code and examples for JHU Computational Genomics class
Crispresso2
⭐
233
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
Snapatac
⭐
227
Analysis Pipeline for Single Cell ATAC-seq
Hgvs
⭐
226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Sortmerna
⭐
220
SortMeRNA: next-generation sequence filtering and alignment tool
Serratus
⭐
219
Ultra-deep search for novel viruses
Roary
⭐
219
Rapid large-scale prokaryote pan genome analysis
Cellbender
⭐
218
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Miso Lims
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214
MISO: An open-source LIMS for NGS sequencing centres
Pycoqc
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213
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
Tradeseq
⭐
206
TRAjectory-based Differential Expression analysis for SEQuencing data
Smudgeplot
⭐
200
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Soapdenovo2
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197
Next generation sequencing reads de novo assembler.
Splatter
⭐
195
Simple simulation of single-cell RNA sequencing data
Single Cell Papers With Code
⭐
193
Papers with code for single cell related papers
Circlator
⭐
193
A tool to circularize genome assemblies
Alignment And Variant Calling Tutorial
⭐
192
basic walk-throughs for alignment and variant calling from NGS sequencing data
Artemis
⭐
191
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Ugene
⭐
190
UGENE is free open-source cross-platform bioinformatics software
Nextclade
⭐
190
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Wgsim
⭐
188
Reads simulator
Minion_qc
⭐
174
Quality control for MinION sequencing data
Snp Sites
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173
Finds SNP sites from a multi-FASTA alignment file
Sccatch
⭐
171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Kubegene
⭐
169
KubeGene - A turn-key Genome Sequencing workflow management framework
Tram
⭐
159
Cross-browser CSS3 transitions in JavaScript.
Insilicoseq
⭐
158
🚀 A sequencing simulator
Afterqc
⭐
157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Sunbeam
⭐
157
A robust, extensible metagenomics pipeline
Genomics
⭐
154
A collection of scripts and notes related to genomics and bioinformatics
Readfish
⭐
152
CLI tool for flexible and fast adaptive sampling on ONT sequencers
Laravel Eloquent Sequencer
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151
A package that allows you to create and manage sequences on Eloquent models.
Awesome Vdj
⭐
150
📚 Tools and databases for analyzing HLA and VDJ genes.
Timingsrc
⭐
149
Source code for timing related libraries managed by webtiming (multi-device timing CG)
Genomicsqlite
⭐
146
Genomics Extension for SQLite
Nextpolish
⭐
145
Fast and accurately polish the genome generated by long reads.
Clairvoyante
⭐
142
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Ngstools
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142
Programs to analyse NGS data for population genetics purposes
Ampliseq
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141
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Nanofilt
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141
Filtering and trimming of long read sequencing data
D4 Format
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139
The D4 Quantitative Data Format
Emp
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136
Code repository of the Earth Microbiome Project.
Sequana
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136
Sequana: a set of Snakemake NGS pipelines
Genomescope
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135
Fast genome analysis from unassembled short reads
Ariba
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135
Antimicrobial Resistance Identification By Assembly
Tcga_example
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135
Gubbins
⭐
133
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Rnaseq Workflow
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133
A repository for setting up a RNAseq workflow
Seq2science
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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.
Alfred
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129
BAM Statistics, Feature Counting and Annotation
Tcr Bcr Seq Analysis
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129
T/B cell receptor sequencing analysis notes
Dna Seq Analysis
⭐
128
DNA sequencing analysis notes from Ming Tang
Game Programming Patterns Cn
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124
游戏编程模式中文
Dragonstar2019
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122
Decontam
⭐
122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Xpore
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122
Identification of differential RNA modifications from nanopore direct RNA sequencing
Dnanalyzer
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122
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
Methylseq
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121
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Compbiodatasetsformachinelearning
⭐
120
A Curated List of Computational Biology Datasets Suitable for Machine Learning
Kairos
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120
A complete framework for data control and composition in the vvvv visual programming environment.
Mirdeep2
⭐
120
Discovering known and novel miRNAs from small RNA sequencing data
Facets
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119
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
V Pipe
⭐
119
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
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