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73 search results found

Extensive de-novo TE Annotator

Shovill ⭐ 104

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

Rnaseqdb ⭐ 83

Say "ni" to data of any size

Orthomcl Pipeline ⭐ 55

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0

Ensembl Hive ⭐ 50

EnsEMBL Hive - a system for creating and running pipelines on a distributed compute resource

Impact Pipeline ⭐ 47

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

microRNA profiling pipeline

Mutation Identification Pipeline. Read the latest documentation:

Metagenomic pipeline and other general scripts used in the lab.

Mtbseq_source ⭐ 32

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

Showspeed ⭐ 28

print I/O activity of process, files, or network.

RNASeq pipeline

Bitacora ⭐ 27

BITACORA: A Bioinformatics tool for gene family annotation

Perl For Bioinformatics ⭐ 26

An attempt to help anyone interested in using Perl for Bioinformatics

Dna Me Pipeline ⭐ 24

DCC/DAC methylation pipeline source

Planttribes ⭐ 23

PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics

Gatb Minia Pipeline ⭐ 22

GATB Minia assembly pipeline

Untangle your unix pipeline one-liners

Integrative ⭐ 19

Software Pipeline for Integrative Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization

Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis

Cancerdiscover ⭐ 17

Open-source software pipeline for cancer classification from high-throughput data using machine learning.

A Shotgun Metagenome Annotation Pipeline

Ci Perl Helpers ⭐ 16

Makes comprehensive testing of Perl projects in Azure Pipelines trivial

Pipedream ⭐ 16

PipeDream - open source neuroimaging pipelines

Circrna_finder ⭐ 14

Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).

icSHAPE pipeline

A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline

Bgi Full Length Rna Analysis Pipeline ⭐ 12

Full-Length RNA Analysis pipeline developted by BGI RD group.

MFannot is a program for the annotation of mitochondrial and plastid genomes

Markdent ⭐ 12

An event-based Markdown parser toolkit

Pangenomepipeline ⭐ 12

PanGenomePipeline

Sars Cov 2_multi Pcr_v1.0 ⭐ 12

SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data

Qbrc Neoantigen Pipeline ⭐ 11

QBRC Neoantigen calling pipeline with CSiN calculation embedded

hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

Illumina analysis pipeline

A clone of the official AMOS git repo on sourceforge: https://sourceforge.net/projects/amos/

Irys Scaffolding ⭐ 10

scripts to parse IrysView output

Damidseq_pipeline ⭐ 10

An automated pipeline for processing DamID sequencing datasets

NGS perl modules

Wgddetector ⭐ 10

Fungal Genome Mapping Pipeline

Trna Read Mapping ⭐ 9

Phylostratigraphy ⭐ 9

Pipeline for Phylostratigraphy

Bgee_pipeline ⭐ 8

Source code of the Bgee pipeline used to build the Bgee database

The ORAC-DR astronomy data reduction pipeline

Perl Utils ⭐ 8

Set of text- and file-oriented utilities for processing texts, files and piping

Somaticwrapper ⭐ 8

Detect somatic variants from tumor and normal WGS/WXS data

Vargenius ⭐ 7

VarGenius is a software for variants discovery and annotation. It allows efficient management of folder data and jobs submission into a PBS cluster. All the variants will be inserted into a PostgreSQL database that can be used for downstream analyses. It is written with PERL, R and HTML languages and uses Picard, Samtools, BWA, GATK and Annovar!

Update_pipeline ⭐ 7

Update a pipelines metadata

Chimeraminer ⭐ 7

ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing.

Os Autoinst Distri Example ⭐ 7

distribution template for openqa tests

Innovation Impact Pipeline ⭐ 7

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

Virusscan ⭐ 7

VirusScan Pipeline

Circos Pipeline ⭐ 7

circos pipeline

Measurement of Allelic Ratio Informatics Operator (MARIO) pipeline

Oxford Plots ⭐ 6

eHive pipeline to build pairwise Oxford plots

Repository for DIYA code

Nextflow pipeline to scan high throughput sequencing data for circRNAs, perform differential expression and generate circRNA-miRNA targets

Cg Pipeline ⭐ 6

Genome assembly/prediction/annotation pipeline for the Linux command line

Genotyping ⭐ 5

Components of the WTSI genotype analysis pipeline.

A pipeline for high-confidence RNA-seq gene co-expression network inference

Perl Powershell ⭐ 5

Ngspipeline ⭐ 5

Nf Repeatmasking ⭐ 5

Nextflow workflow for automatic repeat detection, classification and masking

Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow

Matafiler ⭐ 5

Metagenomic assembly, genome reconstruction and functional as well as taxonomic profiling

A blast-based protein homology pipeline

Ensembl Database Loader ⭐ 5

A eHive Pipeline for loading Ensembl and Ensembl Genomes databases to a MySQL compatible server

Code for statistical binning and related scripts

Deploymentpipeline ⭐ 5

deployment pipeline at AgilaSverige

Clustcompare ⭐ 5

Pipeline to compare secondary metabolite biosynthetic gene clusters (BGCs)

Selection on the Secondary Structure-test: a test that detects positive and negative selection from a set of orthologs, either small or long ncRNAs.

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