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bioinformatics-pipeline

Here are 450 public repositories matching this topic...

scipipe / scipipe

Open

More logging in the globber component

samuell commented May 8, 2021

As reported by @jonalv , it can be confusing what is happening when if the globber pattern does not catch any files.

The suggestion is to:

Log when the globber starts, with the pattern used
Issue a warning if the globber doesn't match any files at all

Read more

enhancement good first issue

Open

Tests do not pass on Windows

grailbio / reflow

A language and runtime for distributed, incremental data processing in the cloud

language golang aws data-science runtime bioinformatics-pipeline scientific-computing cloud-computing analysis-pipeline

Updated Mar 11, 2022
Go

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

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

Updated Mar 7, 2022
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

pysradb

saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

bioinformatics bioinformatics-pipeline ncbi-sra-archive sra ena sratoolkit ncbi-sra

Updated Mar 16, 2022
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 Mar 15, 2022
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

kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

dnase-seq bioinformatics-pipeline atac-seq

Updated Sep 25, 2019
Python

ngless-toolkit / ngless

Open

Add ability to strip sequences/qualities from SAM/BAM files

7

unode commented Feb 28, 2019

When working with very large SAM files it is often convenient to remove sequence and quality information to reduce storage and improve I/O.

Following from this it would be convenient to have a stripSeqQual function that replaces the two fields with *.

Read more

good first issue help wanted

Open

Implement API to cleanup unnecessary files

gcp-for-bioinformatics

lynnlangit / gcp-for-bioinformatics

GCP Essentials for Bioinformatics Researchers

cloud bioinformatics genomics gcp bioinformatics-pipeline bioinformatics-analysis bioinformatics-researchers

Updated Mar 2, 2022
Jupyter Notebook

sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly

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

Updated Jan 31, 2022
Python

yupenghe / methylpy

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

epigenetics bioinformatics-pipeline dna-methylation differential-methylation functional-genomics nome-seq nome-seq-data calling-dmrs

Updated Jul 2, 2021
Python

seq2science

vanheeringen-lab / seq2science

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.

bioinformatics rna-seq snakemake pipeline reproducible-research ngs bioinformatics-pipeline chip-seq atac-seq workflows fastq sra

Updated Mar 17, 2022
Python

MaayanLab / Zika-RNAseq-Pipeline

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

rna-seq pipeline notebook jupyter-notebook bioinformatics-pipeline rna-seq-analysis

Updated Jun 1, 2021
Jupyter Notebook

nickjcroucher / gubbins

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

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

Updated Mar 2, 2022
Python

V-pipe

cbg-ethz / V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

bioinformatics snakemake virus genomics ngs sequencing conda bioinformatics-pipeline hiv sars-cov-2 sarscov2 biohackeu20 biohackcovid20 biohackeu21

Updated Mar 16, 2022
HTML

KarchinLab / open-cravat

A modular annotation tool for genomic variants

javascript python bioinformatics genomics python3 bioinformatics-pipeline annotation-tool variant-annotations variant-annotation variant-analysis genomic-data-analysis bioinformatics-tool

Updated Jan 22, 2022
JavaScript

nsalomonis / altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

python bam-files clustering graphical-interface pagerank bioinformatics-pipeline alternative-splicing command-line-tool splicing-quantification network-analysis pathway-analysis rna-seq-data scrna-seq-data cell-cycle cell-type-classification splicing-visualization fastq-anaysis single-cell-splicing marker-gene-analysis louvain-community-detection

Updated Sep 4, 2021
Python

GregorySchwartz / too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.

visualization bioinformatics-pipeline single-cell bioinformatics-algorithms single-cell-rna-seq single-cell-analysis

Updated Aug 27, 2021
Haskell

biowdl / tasks

A collection of reusable WDL tasks. Category:Other

workflow bioinformatics tasks bioinformatics-pipeline wdl wdl-tasks

Updated Mar 18, 2022
wdl

chanzuckerberg / czid-web

Infectious Disease Sequencing Platform

science bioinformatics research genomics biology sequencing computational-biology next-generation-sequencing bioinformatics-pipeline global-health virology infectious-diseases metagenomic czid chan-zuckerberg-id

Updated Mar 18, 2022
JavaScript

mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data

bioinformatics-pipeline mtdna mt-variant mitochondrial-variants mtoolbox

Updated Feb 25, 2021
Python

ShujiaHuang / ilus

A handy variant calling pipeline generator for whole genome re-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.

bioinformatics ngs vcf bioinformatics-pipeline variant-calling whole-genome-sequencing

Updated Feb 14, 2022
Python

r2g

yangwu91 / r2g

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

bioinformatics bioinformatics-pipeline phylogenetics orthology homology ncbi-sra gene-sequence-retrieval

Updated Apr 2, 2021
Python

urmi-21 / pyrpipe

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

python bioinformatics rna-seq conda bioinformatics-pipeline bioconda bioinformatics-analysis rna-seq-pipeline ncbi-sra rna-seq-workflows

Updated Jun 4, 2021
Python

GenomiqueENS / eoulsan

A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)

java rna-seq analysis workflow-engine bioinformatics-pipeline cloud-computing-clusters

Updated Feb 2, 2022
Java

JetBrains-Research / snakecharm

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

python snakemake intellij eap moment bioinformatics-pipeline pycharm gear bioinformatics-tool intellij-plugins eap-updates platform-ides

Updated Mar 14, 2022
Python

sanger-pathogens / assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

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

Updated Jan 4, 2021
Perl

sanger-pathogens / iva

de novo virus assembler of Illumina paired reads

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

Updated May 17, 2021
Python

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