EXPERIMENT_TITLE: Arima-HiC of human:GM12878
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scale scaffolds. Despite its increasing popularity, there are limited open-source tools available. Errors, particularly inversions and fusions across chromosomes, remain higher than alternate scaffolding technologies. We present a novel open-source Hi-C scaffolder that does not require an a priori estimate of chromosome number and minimizes errors by scaffolding with the assistance of an assembly graph. We demonstrate higher accuracy than the state-of-the-art methods across a variety of Hi-C library preparations and input assembly sizes.
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "NA12878"}, {"TAG": "age", "VALUE": "not collected"}, {"TAG": "biomaterial_provider", "VALUE": "Corriell Institute"}, {"TAG": "sex", "VALUE": "female"}, {"TAG": "tissue", "VALUE": "blood"}, {"TAG": "cell_line", "VALUE": "GM12878"}, {"TAG": "cell_type", "VALUE": "B-Lymphocyte"}, {"TAG": "ethnicity", "VALUE": "caucasian"}, {"TAG": "sample_type", "VALUE": "cell culture"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR6675327.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR006/675/SRR6675327/SRR6675327.sralite.1", "size": "33541735400", "date": "2020-06-24 01:59:59", "md5": "b49aaed301c8ed03ef7176e79ff435c1", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR6675327", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6675327/SRR6675327", "size": "55092762892", "date": "2018-02-06 01:07:42", "md5": "687f8f35a0afa4491475caf2bbc4853e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "GM12878.Arima-HiC.lane1.R2.fastq.gz", "size": "46402062507", "date": "2020-03-05 14:25:52", "md5": "1c0a4166e9f6b4ffcbc2499292185d1d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "GM12878.Arima-HiC.lane1.R1.fastq.gz", "size": "41755531474", "date": "2020-03-05 12:59:55", "md5": "ad88c8d2771b6b01d7b388618c03f637", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]