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TrimGalore Public
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
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Bismark Public
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
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Sherman Public
A simple Bisulfite FastQ Read Simulator (BiQRS)
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nf-core-modules Public
Forked from nf-core/modulesRepository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow MIT License UpdatedNov 30, 2023 -
L1EM Public
Forked from FenyoLab/L1EMEstimate locus specific human LINE-1 expression.
Python Other UpdatedSep 21, 2023 -
simplealign Public
minimal WGS workflow with nf-core tools 2.9dev
Nextflow MIT License UpdatedAug 25, 2023 -
aws_training_images Public
Forked from s-andrews/aws_training_imagesA set of build scripts to generate AWS instances ready to run our training courses
Shell GNU General Public License v3.0 UpdatedAug 24, 2023 -
methylseq Public
Forked from nf-core/methylseqMethylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Nextflow MIT License UpdatedJul 25, 2023 -
nf-WGS Public
A simple workflow to get alignments done. Testing subworkflow setup
Nextflow MIT License UpdatedJun 24, 2023 -
fetchngs Public
Forked from nf-core/fetchngsPipeline to fetch metadata and raw FastQ files from public and private databases. Modifying pigz execution
Groovy MIT License UpdatedApr 25, 2023 -
reStrainingOrder Public
A little QC tool that attempts to predict the genotype of mouse samples used, based on prior knowledge of high-quality SNPs from the Mouse Genomes Project
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bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
Shell MIT License UpdatedFeb 2, 2023 -
SNPsplit Public
Allele-specific alignment sorting
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lightweight-template Public
Forked from ewels/lightweight-templateA minimal Nextflow pipeline that works with @nf-core modules.
Nextflow MIT License UpdatedNov 9, 2022 -
IMPLICON Public
A processing guide for IMPLICON data (bisulfite amplicon data for imprinted loci)
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RinseRepeat Public
A collection of repetitive things...
Perl GNU General Public License v3.0 UpdatedMar 9, 2022 -
TrAEL-seq Public
A collection of software used for the TrAEL-seq manuscript
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illuminaprocessing Public
Forked from s-andrews/illuminaprocessingThe scripts for doing automated run processing from our sequencing facility
Perl UpdatedFeb 7, 2022 -
nextflow_pipelines Public
Forked from s-andrews/nextflow_pipelinesThe set of NGS processing pipelines used at Babraham
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Umi-Grinder Public
The use of UMIs for sequencing becomes more and more frequently used so we need to take them into consideration when deduplicating data aligning to the same positions
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scRepeats Public
Custom script(s) for the processing of files for single-cell repeat analysis
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subset10xbam Public
Forked from s-andrews/subset10xbamA tool to extract subsets of data from the tagged BAM file generated by CellRanger
Python GNU General Public License v3.0 UpdatedApr 27, 2021 -
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test-datasets Public
Forked from nf-core/test-datasetsTest data to be used for automated testing with the nf-core pipelines
MIT License UpdatedJul 15, 2020 -
MultiQC_TestData Public
Forked from MultiQC/test-dataTest data for MultiQC. See https://github.com/ewels/MultiQC
HTML MIT License UpdatedMar 11, 2020 -
Complete-Python-3-Bootcamp Public
Forked from Pierian-Data/Complete-Python-3-BootcampCourse Files for Complete Python 3 Bootcamp Course on Udemy
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deduplicate_by_sequence Public
This script reads paired-end BAM files, and deduplicates alignments based purely on exact matches of the first 50bp of both reads.
Perl UpdatedSep 23, 2019 -
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