Introduction#
pysradb provides a simple method to programmatically access metadata
and download sequencing data from NCBI’s Sequence Read Archive (SRA) and European Bioinformatics
Institute’s European Nucleotide Archive (ENA).
Quick Example#
To fetch metadata associated with project accession SRP265425
$ pysradb metadata SRP265425
study_accession experiment_accession experiment_title experiment_desc organism_taxid organism_name library_name library_strategy library_source library_selection library_layout sample_accession sample_title instrument instrument_model instrument_model_desc total_spots total_size run_accession run_total_spots run_total_bases
SRP265425 SRX8434255 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 63-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745319 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 1311358 83306910 SRR11886735 1311358 109594216
SRP265425 SRX8434254 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 62-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745320 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 2614109 204278682 SRR11886736 2614109 262305651
SRP265425 SRX8434253 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 61-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745318 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 2286312 183516004 SRR11886737 2286312 263304134
SRP265425 SRX8434252 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 60-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745317 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 5202567 507524965 SRR11886738 5202567 781291588
SRP265425 SRX8434251 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 38-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745315 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 3313960 356104406 SRR11886739 3313960 612430817
SRP265425 SRX8434250 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 37-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745316 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 5155733 565882351 SRR11886740 5155733 954342917
SRP265425 SRX8434249 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 36-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745313 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 1324589 175619046 SRR11886741 1324589 216531400
SRP265425 SRX8434248 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 35-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745314 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 1639851 198973268 SRR11886742 1639851 245466005
SRP265425 SRX8434247 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 68-2020-05-07 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745312 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 3921389 210198580 SRR11886743 3921389 332935558
SRP265425 SRX8434246 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 66-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745311 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 14295475 2150005008 SRR11886744 14295475 2967829315
SRP265425 SRX8434245 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 65-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745310 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 5124692 294846140 SRR11886745 5124692 431819462
SRP265425 SRX8434244 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 64-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745309 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 2986306 205666872 SRR11886746 2986306 275400959
SRP265425 SRX8434243 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 34-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745308 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 1182690 59471336 SRR11886747 1182690 86350631
SRP265425 SRX8434242 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 33-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745307 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 6031816 749323230 SRR11886748 6031816 928054297
To fetch detailed metadata which includes link to raw sequencing files, specify --detailed:
$ pysradb metadata SRP265425 --detailed
run_accession study_accession experiment_accession experiment_title experiment_desc organism_taxid organism_name library_name library_strategy library_source library_selection library_layout sample_accession sample_title instrument instrument_model instrument_model_desc total_spots total_size run_total_spots run_total_bases run_alias sra_url_alt1 sra_url_alt2 sra_url experiment_alias isolate collected_by collection_date geo_loc_name host host_disease isolation_source lat_lon BioSampleModel sra_url_alt3 ena_fastq_http ena_fastq_http_1 ena_fastq_http_2 ena_fastq_ftp ena_fastq_ftp_1 ena_fastq_ftp_2
SRR11886735 SRP265425 SRX8434255 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 63-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745319 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 1311358 83306910 1311358 109594216 IonXpress_063_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam gs://sra-pub-src-9/SRR11886735/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886735/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra0/SRR/011608/SRR11886735 GC-20 NA 02-Apr-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/035/SRR11886735/SRR11886735.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/035/SRR11886735/SRR11886735.fastq.gz
SRR11886736 SRP265425 SRX8434254 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 62-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745320 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 2614109 204278682 2614109 262305651 IonXpress_062_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam gs://sra-pub-src-16/SRR11886736/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra46/SRZ/011886/SRR11886736/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta https://sra-download.ncbi.nlm.nih.gov/traces/sra50/SRR/011608/SRR11886736 GC-51 NA 14-Apr-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886736/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/036/SRR11886736/SRR11886736.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/036/SRR11886736/SRR11886736.fastq.gz
SRR11886737 SRP265425 SRX8434253 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 61-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745318 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 2286312 183516004 2286312 263304134 IonXpress_061_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam gs://sra-pub-src-16/SRR11886737/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra29/SRZ/011886/SRR11886737/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta https://sra-download.ncbi.nlm.nih.gov/traces/sra17/SRR/011608/SRR11886737 GC-24 NA 07-Apr-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886737/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/037/SRR11886737/SRR11886737.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/037/SRR11886737/SRR11886737.fastq.gz
SRR11886738 SRP265425 SRX8434252 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 60-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745317 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 5202567 507524965 5202567 781291588 IonXpress_060_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam gs://sra-pub-src-15/SRR11886738/IonXpress_060_R_2020_04_22_15_56_22_user_GCEID_S5_58_SARS_CoV2_SA4.bam.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRZ/011886/SRR11886738/IonXpress_060_R_2020_04_22_15_56_22_user_GCEID_S5_58_SARS_CoV2_SA4.bam https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011608/SRR11886738 GC-23 NA 08-Apr-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886738/IonXpress_060_R_2020_04_22_15_56_22_user_GCEID_S5_58_SARS_CoV2_SA4.bam.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/038/SRR11886738/SRR11886738.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/038/SRR11886738/SRR11886738.fastq.gz
SRR11886739 SRP265425 SRX8434251 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 38-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745315 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 3313960 356104406 3313960 612430817 IonXpress_038_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam gs://sra-pub-src-13/SRR11886739/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886739/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra24/SRR/011608/SRR11886739 GC-11b NA 24-Mar-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/039/SRR11886739/SRR11886739.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/039/SRR11886739/SRR11886739.fastq.gz
SRR11886740 SRP265425 SRX8434250 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 37-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745316 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 5155733 565882351 5155733 954342917 IonXpress_037_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam gs://sra-pub-src-5/SRR11886740/IonXpress_037_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam.1 https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886740/IonXpress_037_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra13/SRR/011608/SRR11886740 GC-14b NA 28-Mar-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/040/SRR11886740/SRR11886740.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/040/SRR11886740/SRR11886740.fastq.gz
SRR11886741 SRP265425 SRX8434249 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 36-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745313 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 1324589 175619046 1324589 216531400 IonXpress_036_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam gs://sra-pub-src-11/SRR11886741/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886741/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011608/SRR11886741 GC-12 NA 24-Mar-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/041/SRR11886741/SRR11886741.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/041/SRR11886741/SRR11886741.fastq.gz
SRR11886742 SRP265425 SRX8434248 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 35-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745314 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 1639851 198973268 1639851 245466005 IonXpress_035_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam gs://sra-pub-src-11/SRR11886742/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886742/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011608/SRR11886742 GC-13 NA 23-Mar-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/042/SRR11886742/SRR11886742.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/042/SRR11886742/SRR11886742.fastq.gz
SRR11886743 SRP265425 SRX8434247 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 68-2020-05-07 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745312 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 3921389 210198580 3921389 332935558 IonXpress_068_R_2020_05_07_11_47_51_user_GCEID-S5-60-SARS_CoV2_SA4.bam gs://sra-pub-src-17/SRR11886743/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRZ/011886/SRR11886743/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/011608/SRR11886743 GC-55 NA 24-Apr-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886743/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/043/SRR11886743/SRR11886743.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/043/SRR11886743/SRR11886743.fastq.gz
SRR11886744 SRP265425 SRX8434246 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 66-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745311 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 14295475 2150005008 14295475 2967829315 IonXpress_066_R_2020_04_22_11_10_56_user_GCEID-S5-57-SARS_CoV2_SA4.fastq gs://sra-pub-src-11/SRR11886744/IonXpress_066_R_2020_04_22_11_10_56_user_GCEID-S5-57-SARS_CoV2_SA4.fastq.1 https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886744/IonXpress_066_R_2020_04_22_11_10_56_user_GCEID-S5-57-SARS_CoV2_SA4.fastq.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra20/SRR/011608/SRR11886744 GC-26 NA 07-Mar-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/044/SRR11886744/SRR11886744.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/044/SRR11886744/SRR11886744.fastq.gz
SRR11886745 SRP265425 SRX8434245 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 65-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745310 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 5124692 294846140 5124692 431819462 IonXpress_065_R_2020_04_22_11_10_56_user_GCEID-S5-57-SARS_CoV2_SA4.bam gs://sra-pub-src-16/SRR11886745/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRZ/011886/SRR11886745/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta https://sra-download.ncbi.nlm.nih.gov/traces/sra19/SRR/011608/SRR11886745 GC-25 NA 10-Apr-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886745/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/045/SRR11886745/SRR11886745.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/045/SRR11886745/SRR11886745.fastq.gz
SRR11886746 SRP265425 SRX8434244 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 64-2020-04-22 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745309 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 2986306 205666872 2986306 275400959 IonXpress_064_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam gs://sra-pub-src-17/SRR11886746/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRZ/011886/SRR11886746/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta https://sra-download.ncbi.nlm.nih.gov/traces/sra47/SRR/011608/SRR11886746 GC-21 NA 03-Apr-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886746/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/046/SRR11886746/SRR11886746.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/046/SRR11886746/SRR11886746.fastq.gz
SRR11886747 SRP265425 SRX8434243 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 34-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745308 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 1182690 59471336 1182690 86350631 IonXpress_034_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam gs://sra-pub-src-16/SRR11886747/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRZ/011886/SRR11886747/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta https://sra-download.ncbi.nlm.nih.gov/traces/sra13/SRR/011608/SRR11886747 GC-11a NA 24-Mar-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886747/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/047/SRR11886747/SRR11886747.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/047/SRR11886747/SRR11886747.fastq.gz
SRR11886748 SRP265425 SRX8434242 Ampliseq of SARS-CoV-2 Ampliseq of SARS-CoV-2 2697049 Severe acute respiratory syndrome coronavirus 2 33-2020-04-03 AMPLICON VIRAL RNA RT-PCR SINGLE SRS6745307 Ion Torrent S5 XL Ion Torrent S5 XL ION_TORRENT 6031816 749323230 6031816 928054297 IonXpress_033_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam gs://sra-pub-src-15/SRR11886748/IonXpress_033_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra43/SRZ/011886/SRR11886748/IonXpress_033_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam https://sra-download.ncbi.nlm.nih.gov/traces/sra66/SRR/011608/SRR11886748 GC-14a NA 28-Mar-2020 Australia: Victoria Homo sapiens COVID-19 swab NA Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886748/IonXpress_033_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/048/SRR11886748/SRR11886748.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/048/SRR11886748/SRR11886748.fastq.gz
See Quickstart for other examples.
Contents#
Publication#
Presentation slides from BOSC (ISMB-ECCB) 2019: https://f1000research.com/slides/8-1183
Citation#
Choudhary, Saket. “pysradb: A Python Package to Query next-Generation Sequencing Metadata and Data from NCBI Sequence Read Archive.” F1000Research, vol. 8, F1000 (Faculty of 1000 Ltd), Apr. 2019, p. 532 (https://f1000research.com/articles/8-532/v1)
@article{Choudhary2019,
doi = {10.12688/f1000research.18676.1},
url = {https://doi.org/10.12688/f1000research.18676.1},
year = {2019},
month = apr,
publisher = {F1000 (Faculty of 1000 Ltd)},
volume = {8},
pages = {532},
author = {Saket Choudhary},
title = {pysradb: A {P}ython package to query next-generation sequencing metadata and data from {NCBI} {S}equence {R}ead {A}rchive},
journal = {F1000Research}
}
Zenodo archive: https://zenodo.org/badge/latestdoi/159590788
Zenodo DOI: 10.5281/zenodo.2306881
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