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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