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90 search results found
Metawrap
⭐
320
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
Pggb
⭐
315
the pangenome graph builder
Flam3
⭐
249
the original fractal flame renderer and genetic language
Merqury
⭐
234
k-mer based assembly evaluation
Gtotree
⭐
174
A user-friendly workflow for phylogenomics
Vgp Assembly
⭐
160
VGP repository for the genome assembly working group
Dna Seq Analysis
⭐
128
DNA sequencing analysis notes from Ming Tang
Genome_updater
⭐
123
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
Tormes
⭐
82
Making whole bacterial genome sequencing data analysis easy
Ggd Recipes
⭐
81
conda recipes for genomic data
Ngseasy
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76
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
Dnabert_2
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72
The official implementation of DNABERT-2.
Mumandco
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49
MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
Genome Data Integration
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35
Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls
Synnet Pipeline
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32
Workflow for Building Microsynteny Networks
Ngsdat2
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28
NGS Data Analysis Textbook Version 2 (Disease Genome Analysis)
Vapid
⭐
27
VAPiD: Viral Annotation and Identification Pipeline
Microbial Informatics 2014
⭐
25
Microbial Whole Genome Sequence data analysis labs for 2014
Comparative_genomics
⭐
24
Micro 612 genomics workshop
Viruspy
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21
A pipeline for viral identification from metagenomic samples
Assembler Components
⭐
20
Components of genome sequence assembly tools
Bioinf545
⭐
20
ATAC-seq lab for BIOINF545
1000g Integration
⭐
19
variant integration methods for the 1000 Genomes Project
Dark_and_camouflaged_genes
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18
Temp2
⭐
18
Algorithm to detect germline and de novo transposon insertions
Extract23
⭐
18
Extract a simulated 23andMe (V3) style file from a Whole Genome BAM file
Mapcomp
⭐
18
Genetic Map Comparison
Encode Ccres
⭐
18
Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements
Syllabus
⭐
18
Genome_assembly
⭐
17
Tracespipe
⭐
16
Reconstruction and analysis of viral and host genomes at multi-organ level
Pipernaseq
⭐
16
A comprehensive pipeline for RNAseq data analysis
Rmap
⭐
15
Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS
Metavic
⭐
15
Virus metagenomic pipeline for unknown host or in absence of a host genome
Splitreader
⭐
15
Split-read pipeline for the identification of non-reference TE insertions with TSDs
Cenote Taker
⭐
14
DEPRECATED: Use Cenote-Taker 3 instead
Bioinformatics Tools
⭐
14
Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files
Ngs_dna
⭐
13
NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC
Genapi
⭐
13
Gene Absence Presence Identification tool.
Viral Assembly
⭐
13
exploring viral genome assembly with variation graph tools
Rna Seq Example
⭐
13
An analysis of Arabidopsis RNA-seq data (hy5 mutant and wt, two replicates each; SRA accession SRX029582)
Docker_bwa_aligner
⭐
13
Docker containers that demonstrate a proof of concept bwa alignment workflow
Setu
⭐
12
SARS-CoV-2 Genome Assembler
Segway
⭐
11
Application for semi-automated genomic annotation.
Dipasm
⭐
11
Illumina Array Protocols
⭐
11
processing illumina SNP arrays
Motifscan
⭐
11
A motif discovery tool to detect the occurrences of known motifs
Plws
⭐
11
Phylogenomics from Low-coverage Whole-genome Sequencing
Cpg_me
⭐
10
A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)
Metagwastoolkit
⭐
10
A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies
Cau Tibetanwheatseq
⭐
10
Customized codes used in Tibetan wheat sequencing project.
Prymetime
⭐
10
Pipeline for Recombinant Yeast genoMEs That Identifies Markers of Engineering
Metagenomicantibioticresistance
⭐
10
NastyBugs: a simple method for extracting antimicrobial resistance information from metagenomes
Piperiboseq
⭐
10
A comprehensive pipeline for Ribo-seq data analysis
Grid
⭐
10
Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
Ngsplotdb
⭐
10
Genome databases generation pipeline for ngs.plot and region_analysis.
Wgs_sample_preparation
⭐
9
Trim, Align to genome, Deduplicate, Realign WGS sequencing samples
Bio598_tutorial
⭐
8
A hands-on tutorial introducing users to reproducible genome reassembly and variant calling
Idc
⭐
8
Simon's Data Club - Reference data for Galaxy servers
Ccontigs
⭐
8
Detect contigs of complete circular genomes
Varscan2
⭐
8
Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
Cometgazer
⭐
8
COMETgazer mehylation analysis software suite
Inpactor
⭐
7
Inpactor: Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons for Large Genomes
Long Read Assembler Test Cases
⭐
7
A small set of test cases for long-read assembly tools
Quivergrid
⭐
7
Quiver wrapper for SGE
Bam_processing
⭐
7
Process SAM/BAM files accroding to the 1k genomes methods
Plot_mitochondrial_genome_with_circos
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7
Wes.wgs
⭐
7
Covid-19 HGI WES/WGS burden test BQC-19 pipeline
Rnaseqfpro
⭐
6
rnaSeqFPro (beta) is a script for full processing of RNASeq data starting from fastq files. It performs fastqc quality control, mapping to the human genome hg19 using STAR second pass, counting with featurecounts using GENCODE gtf annotation, creates master table, performs differential analysis using DESeq2, generates graphs in gglot2.
Impute
⭐
6
Automated imputation pipeline for arbitrary dataset and reference panels.
Rna Seq_mapping_workflow
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6
Pipeline for RNAseq data analysis based on reference genome
Virtual Normal Correction
⭐
6
Set of commandline tools for analysis of tumor variants without a matching normal. Method described in Genome Research: http://genome.cshlp.org/content/25/9/1382.full
Fastq Info
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6
Calculate fastq reads and sequencing coverage
Bioinf525
⭐
6
ATAC-seq lab for BIOINF525
Rmta
⭐
6
Read Mapping and Transcript Assembly
Gb Easy
⭐
6
Bioinformatics pipeline to process genotyping-by-sequencing (GBS) data
Miracum Cbioportal
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6
cBioPortal is a data visualization tool for cancer genomics. This repository contains all components to deploy the customized version of cBioPortal used in the Use Case 3 of MIRACUM in the Medical Informatics Initiative Germany.
1000genomes_selection_exercise
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6
1000 Genomes Selection Exercise
Gapfinisher
⭐
5
A reliable gap filling pipeline for draft genomes
Tadevodrosophila
⭐
5
Code for TAD_SV project
Fenrir
⭐
5
RNA-seq pipeline to detect viral reads
Copycat
⭐
5
Copycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)
Cuttlefishwranglin
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5
Studying the RNA Editing capabilities of Sepia bandensis (dwarf cuttlefish)
Metagenomics Tutorials
⭐
5
Additional scripts from tutorials on tylerbarnum.com
Xenocp
⭐
5
A cloud-based tool for mouse read cleansing in xenograft samples
Ldhat_workflow
⭐
5
Lnisks
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5
Cgb
⭐
5
Custom UCSC Genome Browser
Poolparty
⭐
5
Whole-genome bioinformatic pipeline for pooled or individual-based NGS data using bash and R
Sagawe
⭐
5
⚪ ➡️ 🔍 ℹ️ A suggested workflow, and accompanying scripts, to assemble Single Amplified Genomes (SAGs) from MDA derived Hi/MiSeq (Overlapped) Paired-End Illumina Libraries.
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