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chunlinxiao authored Apr 11, 2023
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Expand Up @@ -31,10 +31,10 @@ Mother:HG004 &nbsp; &nbsp; <sub> https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/g
| <sub>Oxford Nanopore 2D</sub> | <sub>[All](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_HG002_Cornell_Oxford_Nanopore_fasta_fastq_10132015) &nbsp; &nbsp; [HG002](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_HG002_Cornell_Oxford_Nanopore_fasta_fastq_10132015.HG002) </sub> | <sub> - </sub> |
| <sub>Oxford Nanopore ultralong (guppy-V3.2.4_2020-01-22) </sub> | <sub>[All](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_UCSC_ONT_UL_guppy-V3.2.4_2020-01-22) &nbsp; &nbsp; [HG002](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_UCSC_ONT_UL_guppy-V3.2.4_2020-01-22.HG002) </sub> | <sub> minimap2:whatshap:hg19 &nbsp; [All](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_UCSC_ONT_UL_guppy-V3.2.4_2020-01-22.HG002) &nbsp; &nbsp; [HG002](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_UCSC_ONT_UL_guppy-V3.2.4_2020-01-22.HG002) </sub> |
| <sub>Oxford Nanopore ultralong Promethion</sub> | <sub> [All](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_UCSC_ONT_UL_Promethion_03312019) &nbsp; &nbsp; [HG002](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_UCSC_ONT_UL_Promethion_03312019.HG002) &nbsp; &nbsp; [HG003](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_UCSC_ONT_UL_Promethion_03312019.HG003) &nbsp; &nbsp; [HG004](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_UCSC_ONT_UL_Promethion_03312019.HG004) </sub> | <sub> - </sub> |
| <sub>BGI BGISEQ500</sub> | <sub> [All](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_BGISEQ500_01042019) &nbsp; &nbsp; [HG002](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_BGISEQ500_01042019.HG002) </sub> | <sub> - </sub> |
| <sub>BGI MGISEQ PCR-free</sub> | <sub> [All](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_PCRfree_11052018) &nbsp; &nbsp; [HG002](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_PCRfree_11052018.HG002) </sub> | <sub> - </sub> |
| <sub>BGI stLFR</sub> | <sub> [All](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_stLFR_07112018) &nbsp; &nbsp; [HG002](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_stLFR_07112018.HG002) &nbsp; &nbsp; [HG003](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_stLFR_07112018.HG003) &nbsp; &nbsp; [HG004](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_stLFR_07112018.HG004) </sub> | <sub> [All:bwamem:hg19](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_BGI_stLFR_bwamem_GRCh37_07112018) &nbsp; &nbsp; [HG002](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_BGI_stLFR_bwamem_GRCh37_07112018.HG002) &nbsp; &nbsp; [HG003](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_BGI_stLFR_bwamem_GRCh37_07112018.HG003) &nbsp; &nbsp; [HG004](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_BGI_stLFR_bwamem_GRCh37_07112018.HG004)</sub> |
| <sub>Strand-Seq HG002 by BCCRC</sub> | <sub> [All](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_HG002_Strand-seq_BCCRC_04202020) &nbsp; &nbsp; [HG002](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_HG002_Strand-seq_BCCRC_04202020) </sub> | <sub> - </sub> |
| <sub>BGI BGISEQ500</sub> | <sub> [All](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_BGISEQ500_01042019) &nbsp; &nbsp; [HG002](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_BGISEQ500_01042019.HG002) </sub> | <sub> - </sub> |
| <sub>BGI MGISEQ PCR-free</sub> | <sub> [All](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_PCRfree_11052018) &nbsp; &nbsp; [HG002](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_PCRfree_11052018.HG002) </sub> | <sub> - </sub> |
| <sub>BGI stLFR</sub> | <sub> [All](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_stLFR_07112018) &nbsp; &nbsp; [HG002](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_stLFR_07112018.HG002) &nbsp; &nbsp; [HG003](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_stLFR_07112018.HG003) &nbsp; &nbsp; [HG004](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_BGI_MGISEQ_stLFR_07112018.HG004) </sub> | <sub> [All:bwamem:hg19](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_BGI_stLFR_bwamem_GRCh37_07112018) &nbsp; &nbsp; [HG002](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_BGI_stLFR_bwamem_GRCh37_07112018.HG002) &nbsp; &nbsp; [HG003](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_BGI_stLFR_bwamem_GRCh37_07112018.HG003) &nbsp; &nbsp; [HG004](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/alignment.index.AJtrio_BGI_stLFR_bwamem_GRCh37_07112018.HG004)</sub> |
| <sub>Strand-Seq HG002 by BCCRC</sub> | <sub> [All](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_HG002_Strand-seq_BCCRC_04202020) &nbsp; &nbsp; [HG002](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_HG002_Strand-seq_BCCRC_04202020) </sub> | <sub> - </sub> |

<sub> * CompleteGenomics LFR raw or alignment data not available, but analysis results available under: https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/analysis/CompleteGenomics_newLFR_CGAtools_06122015/ </sub>
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