Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

Projects in Awesome Lists tagged with sequencing

A curated list of projects in awesome lists tagged with sequencing .

https://github.com/google/deepvariant

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

bioinformatics deep-learning deep-neural-network deepvariant dna genome genomics machine-learning ngs science sequencing tensorflow

Last synced: 17 Dec 2024

https://github.com/bitfieldaudio/otto

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

audio audio-processing music raspberry-pi sequencing synth synthesizer ui-design

Last synced: 20 Dec 2024

https://github.com/bitfieldaudio/OTTO

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

audio audio-processing music raspberry-pi sequencing synth synthesizer ui-design

Last synced: 10 Nov 2024

https://github.com/opengene/fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi

Last synced: 17 Dec 2024

https://github.com/OpenGene/fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi

Last synced: 14 Nov 2024

https://github.com/broadinstitute/gatk

Official code repository for GATK versions 4 and up

bioinformatics dna gatk genome genomics ngs science sequencing spark

Last synced: 17 Dec 2024

https://github.com/brentp/mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

coverage depth exome genome hacktoberfest nim nim-lang sequencing wgs

Last synced: 17 Nov 2024

https://github.com/hemberg-lab/scRNA.seq.course

Analysis of single cell RNA-seq data course

bookdown course r scrna-seq scrna-seq-analysis sequencing

Last synced: 13 Nov 2024

https://github.com/xebia-functional/fetch

Simple & Efficient data access for Scala and Scala.js

cats concurrency data data-fetching monads monix parallelism scala scala-js sequencing

Last synced: 06 Nov 2024

https://github.com/ideoforms/isobar

A Python package 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 actions.

algorithmic-composition composition midi music sequencing

Last synced: 22 Nov 2024

https://github.com/samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

bam cram dna fasta genomics java java-api ngs sam sequencing vcf

Last synced: 18 Dec 2024

https://github.com/wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

bioinformatics blast genomics genomics-visualization hacktoberfest javascript ruby sequence-alignment sequencing visualization

Last synced: 17 Dec 2024

https://github.com/chanzuckerberg/shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

assembly de-novo dna long-read nanopore pacbio sequencing

Last synced: 13 Nov 2024

https://github.com/nextstrain/nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

clade clades coronavirus covid covid-19 covid19 dna influenza ncov neherlab next-generation-sequencing nextstrain research rna sars-cov-2 science sequences sequencing strain virus

Last synced: 18 Dec 2024

https://github.com/ugeneunipro/ugene

UGENE is free open-source cross-platform bioinformatics software

bioinformatics cpp cross-platform dna msa ngs pipeline qt5 science sequencing ugene workflow

Last synced: 04 Nov 2024

https://github.com/OpenGene/AfterQC

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

adapter-trimming bioinformatics error fastq filtering ngs overlap qc quality-control sequencing trimming

Last synced: 13 Nov 2024

https://github.com/LooseLab/readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers

adaptive-sampling bioinformatics genomics ont oxford-nanopore sequencing

Last synced: 13 Nov 2024

https://github.com/mlin/genomicsqlite

Genomics Extension for SQLite

bioinformatics genomics sequencing sqlite sqlite3

Last synced: 15 Dec 2024

https://github.com/mlin/GenomicSQLite

Genomics Extension for SQLite

bioinformatics genomics sequencing sqlite sqlite3

Last synced: 19 Nov 2024

https://github.com/KairosResearchLab/Kairos

A complete framework for data control and composition in the vvvv visual programming environment.

animation automation blending composition control-systems data-layer interpolation sequencing timeline vl vvvv

Last synced: 10 Dec 2024

https://github.com/zya/beet.js

Polyrhythmic Sequencer library for Web Audio API.

audio js library music sequencing webaudio webaudio-api

Last synced: 26 Oct 2024

https://github.com/OpenGene/gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

bioinformatics consensus deduplication deep-sequencing duplex duplex-sequencing duplication ngs sequencing sequencing-error sequencing-noise somatic

Last synced: 16 Nov 2024

https://github.com/OpenGene/fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

2019-ncov bioinformatics coronavirus covid covid-19 hcov meta-genomics microbial-sequences mngs ngs sars-cov-2 sequencing viral viral-infectious-diseases virus visualization

Last synced: 16 Nov 2024

https://github.com/telatin/seqfu2

:rocket: seqfu - Sequece Fastx Utilities

bioconda bioinformatics bioinformatics-tool fasta fastq genomics ngs sequencing

Last synced: 13 Nov 2024

https://github.com/robertaboukhalil/fastq.bio

An interactive web tool for quality control of DNA sequencing data

bioinformatics fastqc genomics sequencing wasm webassembly

Last synced: 16 Dec 2024

https://github.com/LiuLabUB/HMMRATAC

HMMRATAC peak caller for ATAC-seq data

atac-seq machine-learning peak-caller peak-detection sequencing

Last synced: 16 Nov 2024

https://github.com/tobiasrausch/wally

Wally: Visualization of aligned sequencing reads and contigs

alignment assembly contigs genomics mapping plotting sequencing sequencing-data visualization

Last synced: 07 Nov 2024

https://github.com/tobiasrausch/atacseq

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

atac-seq atac-seq-pipeline chromatin next-generation-sequencing nucleosome-positioning peak-detection sequencing

Last synced: 07 Nov 2024

https://github.com/0xTCG/aldy

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

adme allele bioinformatics cyp2d6 genotype illumina pgrnseq sequencing

Last synced: 25 Oct 2024

https://github.com/robertaboukhalil/ginkgo

Cloud-based single-cell copy-number variation analysis tool

bioinformatics sequencing single-cell-genomics

Last synced: 22 Oct 2024

https://github.com/walaj/bxtools

Tools for analyzing 10X Genomics data

genomics sequencing tenxgenomics

Last synced: 25 Oct 2024

https://github.com/lpantano/seqcluster

small RNA analysis from NGS data

mirna report sequencing smallrna trna

Last synced: 25 Nov 2024

https://github.com/edinburgh-genome-foundry/primavera

:cherry_blossom: Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.

dna-assembly primer-design sequencing synthetic-biology

Last synced: 07 Nov 2024

https://github.com/jamiebuilds/graph-sequencer

Sort items in a graph using a topological sort while resolving cycles with priority groups

adjacency-lists cycles graph priority-list sequencing sorting

Last synced: 26 Oct 2024

https://github.com/cdcgov/tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

azure bioinformatics conda docker genbank genetics liftoff metadata mpox ncbi nextflow nf-tower pipeline python rna-seq scicomp sequencing singularity sra vadr

Last synced: 16 Nov 2024

https://github.com/maragkakislab/samql

SQL-like query language for the SAM/BAM file format

bam bioinformatics go sam sequencing sql

Last synced: 09 Nov 2024

https://github.com/corneliusroemer/desh-data

Sequence lineage information extracted from RKI sequence data repo

dataset germany lineages pangolin robert-koch-institut sars-cov-2 sequencing

Last synced: 14 Oct 2024

https://github.com/jamesseanwright/nanotunes

A small music format and an accompanying implementation using OscillatorNode

music oscillatornode sequencing synthesis web-audio

Last synced: 14 Oct 2024

https://github.com/snijderlab/stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling

antibody mass-spectrometry sequencing

Last synced: 22 Nov 2024

https://github.com/seandavi/ngcgh

Tools for producing pseudo-cgh of next-generation sequencing data

bioinformatics cancer-genomics genomics python sequencing

Last synced: 05 Nov 2024

https://github.com/greenelab/pdx_exomeseq

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

analysis cancer methodology mutation notebook pancreatic-cancer pdx pipeline sequencing wes

Last synced: 13 Nov 2024

https://github.com/sydney-informatics-hub/fastq-to-bam

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

bioinformatics bwa-mem gatk-bestpractices mapping ngs sequencing

Last synced: 21 Nov 2024

https://github.com/pdimens/harpy

Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.

bioinformatics haplotype linked-reads pipeline sequencing variant-calling

Last synced: 08 Dec 2024

https://github.com/tobiasrausch/nrex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

alignment germline mutations sequencing somatic-mutations somatic-variants structural-variation variant-calling

Last synced: 07 Nov 2024

https://github.com/vegaprotocol/wendy

Wendy, the good little fairness widget

blockchain fairness ordering sequencing

Last synced: 12 Nov 2024

https://github.com/ucsd-ccbb/c-view

This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.

epidemiology sequencing viral-genomics

Last synced: 21 Nov 2024

https://github.com/achillesrasquinha/16smart

16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).

16s-rrna bioinformatics meta-analysis mothur python reproducible-research sequencing

Last synced: 13 Nov 2024

https://github.com/nasa-ammos/seq-json-schema

Standardized JSON Schema for authoring multi-mission sequences.

aerospace command json-schema modeling multi-mission nasa planning schema sequence sequencing spacecraft

Last synced: 05 Nov 2024

https://github.com/rtahmasbi/geneevolve

A fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data

bioinformatics cpp genomics sequencing simulator snp-data statistics

Last synced: 08 Nov 2024

https://github.com/dhimmel/fratjuice

Uncovering the microbes of fraternity basements

fraternity fratjuice microbiome sequencing ubiome

Last synced: 14 Oct 2024

https://github.com/cpanse/nestlink

Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles - replication code

bioconductor mass-spectrometry prediction retention-time rpackage sequencing simulation

Last synced: 15 Dec 2024

https://github.com/robaina/genbankpy

Tools to download, parse and filter GenBank files

bioinformatics computational-biology genbank genomics ncbi python sequencing

Last synced: 27 Oct 2024

https://github.com/sam-k/seq-quality-trimming

Trimming Sanger sequencing reads by quality

dna genomics metabarcoding sequencing ta-cloning

Last synced: 29 Nov 2024

https://github.com/poisonalien/basecounts

A tool to extract ATGC/Indel read counts at user specific loci from BAM files

bam basecounts bioinformatics nucleotide-frequency readcounts sequencing wgs-data

Last synced: 24 Oct 2024

https://github.com/bioinfo-chru-strasbourg/stark

STARK is a Next-Generation Sequencing data analysis pipeline for clinical diagnosis

clinic diagnosis docker genetic ngs sequencing

Last synced: 17 Nov 2024

https://github.com/tobiasrausch/rdxon

Reference-free FASTQ filter for rare germline and somatic variants

cancer-genomics k-mer pan-genome rare-disease reference-free sequencing variant-calling

Last synced: 14 Oct 2024

https://github.com/tomwhite/disq-original

A library for manipulating bioinformatics sequencing formats in Apache Spark.

bioinformatics genomics ngs sequencing spark

Last synced: 18 Dec 2024

https://github.com/pseudogene/docker-stacks

Stacks is a software pipeline for building loci from short-read sequences - Now in a Docker

bioinformatics docker-image docker-stacks genetics rad sequencing

Last synced: 13 Dec 2024

https://github.com/ambuvjyn/baseq

Basic Sequence Processing Tool for Biological Data is a set of functions used in bioinformatics to analyze DNA or RNA sequences, perform tasks such as cleaning sequences, counting nucleotides, calculating GC content, generating reverse complements, and translating sequences to protein to just name a few.

bioinformatics r sequencing

Last synced: 28 Oct 2024

https://github.com/gauravcodepro/genotyping-platform

a custom function which can be used to prepare the files for the genotyping or the sequencing. You can specify the path and the fasta files and mark them according to the desired condition for the genotyping or sequencing

genome-sequencing genomes genotyping sequencing sequencing-data sequencing-reads

Last synced: 09 Nov 2024

https://github.com/shashwat9kumar/rna_sequencing_and_genome_analysis

A project to sequence the RNA from actual error prone reads from a PCR process and then to analyze the sequenced protein sequence

cpp dna dna-sequences gnuplot graph-theory pcr-process rna rna-seq-analysis sequencing

Last synced: 13 Nov 2024

https://github.com/alexandervrs/extimeline

A better timeline system for GameMaker Studio 1.x

game-development game-maker game-maker-studio sequencing timeline timing

Last synced: 20 Nov 2024

https://github.com/cometsong/mbiome_seqrun_qc

List of sequencer runs; QC and run Info from each run, modular display of all existing (uploaded) types of info and statistics.

16s 16s-rrna flask microbiome mwgs ngs-pipeline python3 qc sequencing

Last synced: 20 Nov 2024

https://github.com/ethanmclark1/kpnn

Knowledge-Primed Neural Network (KPNN) is a deep learning model designed to predict T-cell receptor (TCR) signaling using gene expression data. By leveraging domain knowledge in the form of a gene hierarchy, KPNN constructs a computational graph that mirrors the biological network, enabling interpretable results and improved accuracy.

bioinformatics biology computational-biology gene-expression interpretability knowledge-primed neural-network sequencing t-cell-receptor tensorflow

Last synced: 25 Nov 2024

https://github.com/chrisarg/bio-seqalignment-components-sundry

Various components for building RNA sequencing applications in Perl

bioinformatics fasta fastq rna-seq sequence-alignment sequencing

Last synced: 03 Dec 2024

https://github.com/sirselim/alkresbaz_keystory_2020

My Key Story presentation for Auckland Research Bazaar 2020

genomics nanopore-sequencing sequencing

Last synced: 07 Dec 2024

https://github.com/pmuens/biostar

Environment to practice Bioinformatics

bioinformatics dna dna-sequences rna rna-seq sequencing

Last synced: 17 Oct 2024

https://github.com/gauravcodepro/bcftools-filter

making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.

bioinformatics-algorithms oxford-nanopore pacbio-data pacbio-sequencing sequencing variant-analysis variant-calling variants

Last synced: 09 Nov 2024

https://github.com/vjcitn/omicidxclient

R functions for querying Sean Davis' omicidx system

metadata sequencing sra

Last synced: 11 Nov 2024