Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections.
The 1000 Genomes Phase 3 data can be downloaded in hg19 coordinates from the FTP site below: Single-end reads: lobSTR -f FILE1,FILE2,.. \ --index-prefix PATH_TO_Index/lobSTR_ \ -o Output_Prefix \ --rg-sample Sample \ --rg-lib LIB Paired-end reads: lobSTR --p1 FILE1,FILE2,.. --p2 FILE1,FILE2,.. \ --index-prefix PATH_TO_Index/lobSTR… Roddy RNA-seq Workflow Plugin. Contribute to DKFZ-ODCF/RNAseqWorkflow development by creating an account on GitHub. Contribute to stormlovetao/xQTLimp development by creating an account on GitHub. By default, peddy uses hg19/GRCh37. It can be forced to use sites for hg38 by passing --sites hg38. To create custom sites, have a look at the sites files included with peddy along with the corresponding .bin.gz which is just the raw binary… Scripts for downloading reference genomes and annotations - gwcbi/cbi_reference_genomes The file must have the original format provided by gencode, gzipped files are not supported.
Implementation of structural variant finding algorithm arriba by Sebastian Uhrig - BD2KGenomics/dockstore_tool_arriba -o * output directory -r * reference genome -v * VCF file or directory --gz flag denoting VCF files are gzipped --rnaedit ** flag to N-mask rna editing sites -e ** file containing RNA editing sites, can be downloaded from Radar (http… C++ htslib/bwa-mem/fermi interface for interrogating sequence data - walaj/SeqLib hg19.bowtie2_index/hg19_trans/hg19_known_ensemble_trans.* How to get: download from (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) or follow instructions provided by bowtie2. Runs STARFusion and arriba. Contribute to BD2KGenomics/dockstore_workflow_fusion development by creating an account on GitHub. python radia.py patientId chrom -n normalDnaBamFilename.bam -t tumorDnaBamFilename.bam -r tumorRnaBamFilename.bam -f hg19.fa --rnaTumorUseChr --rnaTumorFasta=hg19_w_chr_prefix.fa -o /radia/raw/patientId_chr1.vcf.gz -i hg19 -u http://url_to… Contribute to mcfrith/tandem-genotypes development by creating an account on GitHub.
rvtest --inVcf input.vcf --pheno phenotype.ped --out output --geneFile refFlat_hg19.txt.gz --burden cmc --vt price --kernel skat,kbac Snakemake pipeline for processing single-cell combinatorial indexing ATAC seq data - BIMSBbioinfo/scipipeline Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing - aquaskyline/Clairvoyante Rapid Elimination of Useless Sequences. Contribute to schorlton/Reuse development by creating an account on GitHub. Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation) - KHP-Informatics/ngseasy The output is provided as a gzipped file 'Labels.tsv.gz' with columns chromosome, start position, and label. This output file together with a protocol of the tool run is saved to the specified output directory. A pair of Gzipped FastQ files or an HG19/HG38 aligned BAM file. These can be generated from whole genome sequencing, whole exome sequencing, or RNA-Seq.
Software program for checking sample matching for NGS data - parklab/NGSCheckMate
Single-end reads: lobSTR -f FILE1,FILE2,.. \ --index-prefix PATH_TO_Index/lobSTR_ \ -o Output_Prefix \ --rg-sample Sample \ --rg-lib LIB Paired-end reads: lobSTR --p1 FILE1,FILE2,.. --p2 FILE1,FILE2,.. \ --index-prefix PATH_TO_Index/lobSTR… Roddy RNA-seq Workflow Plugin. Contribute to DKFZ-ODCF/RNAseqWorkflow development by creating an account on GitHub. Contribute to stormlovetao/xQTLimp development by creating an account on GitHub. By default, peddy uses hg19/GRCh37. It can be forced to use sites for hg38 by passing --sites hg38. To create custom sites, have a look at the sites files included with peddy along with the corresponding .bin.gz which is just the raw binary… Scripts for downloading reference genomes and annotations - gwcbi/cbi_reference_genomes