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1 RNA Sequencing Pipeline RNA_DEG_PIPELINE_USING_VOOM_VER_1 Quality checking Adaptive trimming Transcripts indexing BAM aligning BAM file replacing BAM sorting BAM indexing Statistics calculating Transcripts indexing Transcripts building Chromosome GTF file sorting_ Bed file coverting BAM Sorting Transcriptome coordinates translating BAM filtering Transcriptome aligning and calculating Making Matrix for limma voom Mean_variance estimating Precision weight generating hgh87 상세보기
2 WGS Sequencing Pipeline VARIANT_CALLING_PIPELINE_USING_SNPEFF_VER_1 Identifying genomic variants such as single nucleotide polymorphisms and DNA insertions and deletions can play an important role in scientific discovery_ To this end a pipeline has been developed to allow researchers at the CGSB to rapidly identify and annotate variants_ The pipeline employs the Genome Analysis Toolkit to perform variant calling and is based on the best practices for variant discovery analysis outlined by the Broad Institute_ Once SNPs have been identified_ SnpEff is utilized to annotate and predict the effects of the variants hgh87 상세보기
3 RNA Sequencing Pipeline RNA_DEG_PIPELINE_USING_CUFFPACKAGE_VER_1 Quality checking Adaptive trimming BAM aligning Transcripts indexing Redundancy removing BAM indexing Transcripts comparing Differential Expression hgh87 상세보기
4 Sequence Alignment Pipeline LAST_PIPELINE_VER_1 LastDB _ This program prepares sequences for subsequent comparison and alignment using lastal LastAL _ This program finds local alignments between query sequences_ and reference sequences that have been prepared using lastdb_ LastSplit _ This program estimates _split alignments_ _typically for DNA_ or _spliced alignments_ _typically for RNA__ If you run split module for whole genome maf file_ you have to run maf_swap module after the split module_ And then you have to run split module again for accuracy of alignment LastSwap _ This will align each rat base_pair to at most one cat base_pair_ but not necessarily vice_versa_ We can get 1_to_1 alignments by swapping the sequences and running last_split again_ If you run maf_swap module for whole genome maf file_ you have to run split module after the maf_swap module_ And then you have to run maf_swap module again LastConvert _ This script reads alignments in maf format_ and writes them in another format_ It can write them in these formats_ axt_ blast_ blasttab_ html_ psl_ sam_ tab_ _If it is protein data_ you have to choice psl hgh87 상세보기
5 Sequence Alignment Pipeline CLUSTALO_PIPELINE_VER_1 Clustao is a general purpose multiple sequence alignment program hgh87 상세보기
6 Metagenomics Pipeline INTERPROSCAN_PIPELINE_VER_1 Users who have novel nucleotide or protein sequences that they wish to functionally characterise can use the software package InterProScan to run the scanning algorithms from the InterPro database in an integrated way. Sequences are submitted in FASTA format. Matches are then calculated against all of the required member database's signatures and the results are then output in a variety of formats hgh87 상세보기
7 RNA Sequencing Pipeline RNA_DEG_PIPELINE_USING_CUFFPACKAGE_VER_2 Quality checking Adaptive trimming BAM aligning Transcripts indexing Redundancy removing BAM indexing Transcripts comparing Differential Expression hgh87 상세보기
8 Hadoop Base Analysis Pipeline HADOOP_BIG_BWA_MEM_PIPELINE_VER_1 Hadoop to boost the performance of the Burrows Wheeler Aligner. BWA works by seeding alignments with maximal exact matches MEMs and then extending seeds with the affine gap Smith Waterman algorithm SW hgh87 상세보기
9 Hadoop Base Analysis Pipeline HADOOP_SPARK_BWA_MEM_PIPELINE_VER_1 SparkBWA is a tool that integrates the Burrows Wheeler Aligner_ BWA on a Apache Spark framework running on the top of Hadoop hgh87 상세보기
10 Epigenome Analysis Pipeline EPIGENOME_ANALYSIS_PIPELINE_USING_HOMER_VER_2 Quality chek of a raw file using FastQC Filtering reads with low quality scores using fastq_quality_filter Quality check of a filtered files using FastQC Alignment using Bowtie Peak calling using MACS Annotation using annotatePeaks Visualization using make UCSCfile hgh87 상세보기