RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon - NCBI-Hackathons/rnaseqview Small library for persistent identifiers used in scholarly communication. sri = read.csv("SraRunInfo.csv", stringsAsFactors=False) keep = grep("CG8144|Untreated-",sri$LibraryName) sri = sri[keep,] fs = basename(sri$download_path) for(i in 1:nrow(sri)) download.file(sri$download_path[i], fs[i]) names(sri) [1] "Run… In this post I’ll try to make an argument for archiving data in the SRA through demonstration of the sratools wrapper from the ipyrad.analysis toolkit, which makes it easy and elegant to download data from the SRA when working in Python… Contribute to leekgroup/SRAmetadata development by creating an account on GitHub. Contribute to farsightsec/axamd_client development by creating an account on GitHub.
The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools.
RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon - NCBI-Hackathons/rnaseqview Small library for persistent identifiers used in scholarly communication. sri = read.csv("SraRunInfo.csv", stringsAsFactors=False) keep = grep("CG8144|Untreated-",sri$LibraryName) sri = sri[keep,] fs = basename(sri$download_path) for(i in 1:nrow(sri)) download.file(sri$download_path[i], fs[i]) names(sri) [1] "Run… In this post I’ll try to make an argument for archiving data in the SRA through demonstration of the sratools wrapper from the ipyrad.analysis toolkit, which makes it easy and elegant to download data from the SRA when working in Python… Contribute to leekgroup/SRAmetadata development by creating an account on GitHub.
Contribute to MWJMerkx/pcfb_project development by creating an account on GitHub.
sri = read.csv("SraRunInfo.csv", stringsAsFactors=False) keep = grep("CG8144|Untreated-",sri$LibraryName) sri = sri[keep,] fs = basename(sri$download_path) for(i in 1:nrow(sri)) download.file(sri$download_path[i], fs[i]) names(sri) [1] "Run… In this post I’ll try to make an argument for archiving data in the SRA through demonstration of the sratools wrapper from the ipyrad.analysis toolkit, which makes it easy and elegant to download data from the SRA when working in Python… Contribute to leekgroup/SRAmetadata development by creating an account on GitHub. Contribute to farsightsec/axamd_client development by creating an account on GitHub. Contribute to NCBI-Hackathons/TCGA_dbGaP development by creating an account on GitHub. Package for fetching metadata and downloading data from SRA - saketkc/pysradb
For example, you can find the SRA file SRR390728.sra in ~/ncbi/sra and the resource files in ~/ncbi/refseq. Then you can run other SRA tools, e.g. fastq-dump on computing nodes.
Downloading read data from ENA The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. CSBB - Computational Suite For Bioinformaticians and Biologists - csbbcompbio/CSBB-v3.0
In this post I’ll try to make an argument for archiving data in the SRA through demonstration of the sratools wrapper from the ipyrad.analysis toolkit, which makes it easy and elegant to download data from the SRA when working in Python… Contribute to leekgroup/SRAmetadata development by creating an account on GitHub. Contribute to farsightsec/axamd_client development by creating an account on GitHub. Contribute to NCBI-Hackathons/TCGA_dbGaP development by creating an account on GitHub. Package for fetching metadata and downloading data from SRA - saketkc/pysradb Rapid, in silico characterization of Bacillus cereus group isolates using WGS data - lmc297/BTyper Contribute to pivotbio/sra-observatory development by creating an account on GitHub.
Python package for interacting with SRAdb and downloading datasets from SRA. pysradb can utilize a SQLite database file that has preprocessed metadata made available by pysradb makes it super easy to download datasets from SRA.
MetaSRA: normalized sample-specific metadata for the Sequence Read Archive - deweylab/MetaSRA-pipeline This script provides replication of certain utilities from the discontinued SRDF Adapter Utilities plugin - adahn6/sra-utilities-script Scripts to download isolates attached to a NCBI Bioproject, Taxonomy ID from ENA or simply a list of accession ids with their metadata - yosoyubik/NCBI-Downloader