INSDC Reference Sequence Public Dataset Tutorial

The INSDC Reference Sequence Public Dataset enables access to biological reference sequences submitted to the INSDC, where sequences are identified according to checksum. The dataset includes both raw sequence as well as associated metadata.

Accessing Data

insdc-reference-sequences
|-- sequence
|   |-- 023e92ccde5f86f31ea0844a92dddb86
|   |-- 8238c4f8a7915991ac98d769837f9b4b91da2a2297598e50
|   |-- bf237796417701948b5f6005d72ca5a0376f3c89e95a1c4f
|   |-- c2424a8ffca9cf8f9ef46cfdd5f69efede74b44e820c178a
|   |-- dbe6100b83178f3ac561d98c2dfc41a0
|   |-- ff734bf70e13affa85a272fda6659a5f
|   |__ *
|__ metadata
    |-- json
    |   |-- 023e92ccde5f86f31ea0844a92dddb86.json
    |   |-- 8238c4f8a7915991ac98d769837f9b4b91da2a2297598e50.json
    |   |-- bf237796417701948b5f6005d72ca5a0376f3c89e95a1c4f.json
    |   |-- c2424a8ffca9cf8f9ef46cfdd5f69efede74b44e820c178a
    |   |-- dbe6100b83178f3ac561d98c2dfc41a0
    |   |-- ff734bf70e13affa85a272fda6659a5f
    |   |__ *.json
    |__ csv
        |-- AAIYXD01.full.csv
        |-- CABIKC01.full.csv
        |-- LVHX01.full.csv
        |__ *.full.csv

CSV logs

Logs of upload processing events are available from s3://PDS/metadata/csv. Each file represents a single load attempt (generally containing all sequences in an assembly), and each line is a loaded sequence. The following table outlines data columns for each sequence record.

Loaded sequence columns in metadata CSV

#	Field Name	Description	Example
1	trunc512	Secure Hash Algorithm (SHA) 512-bit hex-string digest of sequence, truncated to 48 characters	`b9046fc3fb417f114d7e108637c448b2` `14d78b7a5e345c7c`
2	md5	Message Digest (MD5) hex-string digest of sequence (32 characters)	`cd8d02e2d8af721bed2ba9392a96da0e`
3	length	Sequence base pair length	1470266
4	sha512	Secure Hash Algorithm (SHA) 512-bit hex-string digest of sequence (128 characters)	`b9046fc3fb417f114d7e108637c448b2` `14d78b7a5e345c7c1d527fd895f081d1` `109da900101f323d142a407ef22cbfb6` `c2a174eb796217d1afa7fbbe1564787a`
5	trunc512_base64	Base64 representation of `trunc512` digest (32 characters)	`uQRvw_tBfxFNfhCGN8RIshTXi3peNFx8`
6	insdc	INSDC Versioned Accession Number	CABIKC010000001.1
7	ena_type	Record type	expanded_con
8	species	Human readable species taxonomic name (ie. Genus species)	"Saccharomyces cerevisiae"
9	biosample	BioSample Accession	SAMEA5816324
10	taxon	NCBI Taxonomy species identifier	4932

An example csv of loaded sequences is displayed below as a table. The table shows a subset of sequences from assembly GCA_902192315.1, a Saccharomyces cerevisiae genome assembly.

Example CSV of loaded sequences from assembly GCA_902192315.1

`trunc512`	`md5`	`length`	`sha512`	`trunc512_base64`	`insdc`	`ena_type`	`species`	`biosample`	`taxon`
`b9046fc3fb417f114d7e108637c448b214d78b7a5e345c7c`	`cd8d02e2d8af721bed2ba9392a96da0e`	`1470266`	`b9046fc3fb417f114d7e108637c448b214d78b7a5e345c7c1d527fd895f081d1109da900101f323d142a407ef22cbfb6c2a174eb796217d1afa7fbbe1564787a`	`uQRvw_tBfxFNfhCGN8RIshTXi3peNFx8`	`CABIKC010000001.1`	`expanded_con`	`"Saccharomyces cerevisiae"`	`SAMEA5816324`	`4932`
`8decdfa7b43090448ae9411a77e2105390855bd0770e0ded`	`fa6ea9d18d255f0586cf967071bacf8a`	`1062691`	`8decdfa7b43090448ae9411a77e2105390855bd0770e0ded4ec8d19bc17e0d2c2af4c9c38c694502d061bd310547020df5ded87641450a20a6e24985bef5904c`	`jezfp7QwkESK6UEad-IQU5CFW9B3Dg3t`	`CABIKC010000002.1`	`expanded_con`	`"Saccharomyces cerevisiae"`	`SAMEA5816324`	`4932`
`e64dd23642d2f4fcd9646eaf844f8b1b66e8dc6ca7199e14`	`e6d87174b53bc10a65e8b30363fe994f`	`1092091`	`e64dd23642d2f4fcd9646eaf844f8b1b66e8dc6ca7199e143e84b54652c583958f642604497bdfcf5491c9879da9b8d3e46b8a3f010859e0d27367ab82f7c808`	`5k3SNkLS9PzZZG6vhE-LG2bo3GynGZ4U`	`CABIKC010000003.1`	`expanded_con`	`"Saccharomyces cerevisiae"`	`SAMEA5816324`	`4932`
`b9cc12a05937d362b5a55dc4a38850782c034cdf682bd465`	`178f3cd414e0f23b97397f705fade52d`	`912642`	`b9cc12a05937d362b5a55dc4a38850782c034cdf682bd465078fc5bbb321b09c4ad3f9717c52778d08ffb03673c317e3ab18836d110f1db86965c1840ee0bb66`	`ucwSoFk302K1pV3Eo4hQeCwDTN9oK9Rl`	`CABIKC010000004.1`	`expanded_con`	`"Saccharomyces cerevisiae"`	`SAMEA5816324`	`4932`
`ae6c673a1878afc4bf4a2df1ed9667d116e1e294015f8875`	`bba885139f4796326100ff9db55b9235`	`815240`	`ae6c673a1878afc4bf4a2df1ed9667d116e1e294015f8875c6db3be3b313adb9f854b41d10faf4cc796621640158eef5b9f467dd4ff107b7bd9988f5be105b16`	`rmxnOhh4r8S_Si3x7ZZn0Rbh4pQBX4h1`	`CABIKC010000005.1`	`expanded_con`	`"Saccharomyces cerevisiae"`	`SAMEA5816324`	`4932`

How to Start Using the Data

Download Sequence and Metadata

curl

You can download sequences/metadata via the curl command-line tool. Be sure to include the -L flag, which will redirect to sequence content (stored under the TRUNC512 id file) from the MD5 id file.

curl -L http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/sequence/dbe6100b83178f3ac561d98c2dfc41a0
curl -L http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/metadata/json/dbe6100b83178f3ac561d98c2dfc41a0.json

Python

You can use the requests library in Python to download sequences and metadata.

import requests

url_sequence = "http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/sequence/dbe6100b83178f3ac561d98c2dfc41a0"
response_sequence = requests.get(url_sequence)
print(response_sequence.content)

url_metadata = "http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/metadata/json/dbe6100b83178f3ac561d98c2dfc41a0.json"
response_metadata = requests.get(url_metadata)
print(response_metadata.content)

R

You can use the httr library in R to download sequences and metadata.

library(httr)

url.sequence <- "http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/sequence/dbe6100b83178f3ac561d98c2dfc41a0"
response.sequence <- GET(url.sequence)
content(response.sequence, "text")

url.metadata <- "http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/metadata/json/dbe6100b83178f3ac561d98c2dfc41a0.json"
response.metadata <- GET(url.metadata)
content(response.metadata, "text")

Java

String sequence = "http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/sequence/dbe6100b83178f3ac561d98c2dfc41a0";
URL urlSequence = new URL(sequence);
HttpURLConnection connectionSequence = (HttpURLConnection) urlSequence.openConnection();
connectionSequence.setRequestMethod("GET");

String metadata = "http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/metadata/json/dbe6100b83178f3ac561d98c2dfc41a0.json"
URL urlMetadata = new URL(metadata);
HttpURLConnection connectionMetadata = (HttpURLConnection) urlMetadata.openConnection();
connectionMetadata.setRequestMethod("GET");

Locate sequence identifiers from CSV data

Given a genome assembly of interest, the csv data can be used to get checksums, and therefore raw sequence, for all sequences in the assembly. For example, to locate all sequences for assembly GCA_902192315.1, we can request the following to access the CSV:

curl -L http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/metadata/csv/CABIKC01.full.csv

The first and second columns of the resulting csv give us the TRUNC512 and MD5 identifiers, respectively, of all sequences in the assembly. We can use either identifier to download each sequence. Given that the first sequence has a TRUNC512 id of b9046fc3fb417f114d7e108637c448b214d78b7a5e345c7c, we can request:

curl -L http://ga4gh-refget.s3-website.us-east-2.amazonaws.com/sequence/b9046fc3fb417f114d7e108637c448b214d78b7a5e345c7c

The above process can be repeated for all sequences to collect and reconstruct the entire assembly.

jb-adams/TUTORIAL.md

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