#

sequencing

Here are 314 public repositories matching this topic...

google / deepvariant

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

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

Updated Dec 10, 2021
Python

bitfieldaudio / OTTO

Open

Sampler Graphics

3

jmidt commented Aug 19, 2019

We need some good graphics for the main sampler screen. This is where you can do rudimentary editing of the samples that are played in the sequencer.
There are two screens. The main screen with the controls:

Volume (this one may be changed later)
Speed (Playspeed. The sample also pitches up or down)
Filter (in the middle the sound is unchanged, away from center it engages either hi-pass

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graphics good first issue

Open

UI templates

8

Open

Implement a DIRECT FORM I biquad filter in Gamma

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OpenGene / fastp

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

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

Updated Dec 22, 2021
C++

broadinstitute / gatk

Official code repository for GATK versions 4 and up

java science bioinformatics spark genomics genome cluster ngs sequencing gatk-jar dna gatk

Updated Dec 22, 2021
Java

galaxyproject / galaxy

Data intensive science for everyone.

docker science workflow bioinformatics pipeline genomics workflow-engine ngs sequencing dna usegalaxy hacktoberfest

Updated Dec 23, 2021
Python

hemberg-lab / scRNA.seq.course

Analysis of single cell RNA-seq data course

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

Updated Aug 10, 2021
TeX

47degrees / fetch

Simple & Efficient data access for Scala and Scala.js

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

Updated Dec 22, 2021
Scala

brentp / mosdepth

Sponsor

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

coverage nim genome sequencing depth wgs hacktoberfest exome nim-lang

Updated Jul 19, 2021
Nim

ideoforms / isobar

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.

music midi composition sequencing algorithmic-composition

Updated Jun 7, 2021
Python

chanzuckerberg / shasta

De novo assembly from Oxford Nanopore reads.

nanopore assembly sequencing dna long-read pacbio de-novo

Updated Dec 17, 2021
C++

samtools / htsjdk

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

java genomics gradle intellij jar ngs sequencing oracle sam vcf dna java-api fasta bam failure cram htsjdk

Updated Dec 22, 2021
Java

wurmlab / sequenceserver

Open

Add "share" link on the left under downloads

yannickwurm commented Dec 19, 2021

It isn't obvious to users that a search result URL is stable (until deleted).

To make this more obvious, we should add an explicit
Share results section, with a "Copy URL to clipboard" text that does what it says

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feature good first issue

Open

Non-executable files set with executable permissions

2

Open

bed or gff alternate table format outputs

1

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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

machine-learning-algorithms sequencing epigenetics bioinformatics-pipeline single-cell-analysis single-cell-atac-seq

Updated Oct 1, 2021
R

twbattaglia / RNAseq-workflow

A repository for setting up a RNAseq workflow

science workflow bioinformatics rna-seq pipeline sequencing genes

Updated Apr 10, 2017
R

sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Updated Sep 26, 2020
Perl

OpenGene / AfterQC

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

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

Updated May 14, 2020
Python

biocommons / hgvs

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

bioinformatics genomics sequencing

Updated Dec 18, 2021
Python

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Updated Dec 16, 2020
C

sanger-pathogens / Artemis

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

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Updated Nov 11, 2021
Java

sanger-pathogens / circlator

A tool to circularize genome assemblies

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Updated Nov 2, 2021
Python

ugene

ugeneunipro / ugene

UGENE is free open-source cross-platform bioinformatics software

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

Updated Dec 23, 2021
C++

mercury

tmhglnd / mercury

A minimal and human-readable language and environment for the live coding of algorithmic electronic music.

language performance osc creative-coding sequencing live-coding livecoding visuals mercury algorithmic-composition sounds mercury-environment human-readable-language

Updated Nov 30, 2021
Max

genomics

igordot / genomics

A collection of scripts and notes related to genomics and bioinformatics

science workflow bioinformatics nanopore genomics sequencing vcf dna fasta gtf illumina fastq fast5

Updated Oct 7, 2021
R

nextstrain / nextclade

Open

Clade graph needs updating for Omicron and Delta 21I/J

5

corneliusroemer commented Dec 21, 2021

This is how it looks right now, we need to add 21H (Mu), 21 I/J (Delta), 21 K/L/M (Omicron)

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good first issue help wanted package: nextclade_web prio: low

Open

Rebuild `nextstrain/base` Docker image automatically?

Open

Allow for reverse-complemented input sequences

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sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Updated Dec 18, 2021
Python

mlin / GenomicSQLite

Genomics Extension for SQLite

bioinformatics genomics sqlite sequencing sqlite3

Updated Nov 3, 2021
C++

HadrienG / InSilicoSeq

🚀 A sequencing simulator

bioinformatics simulation sequencing metagenomics illumina-sequencing

Updated Oct 13, 2021
Python

cLoops

YaqiangCao / cLoops

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

Updated Dec 8, 2020
Python

ZJUFanLab / scCATCH

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

rna-seq sequencing transcriptome transcriptomics single-cell marker-genes seurat cluster-annotation cell-markers

Updated Sep 23, 2020
R

tobiasrausch / alfred

BAM Statistics, Feature Counting and Annotation

alfred quality quality-control sequencing read-counts insert-size coverage-distribution alignment-metrics feature-counting

Updated Dec 15, 2021
C++

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