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.
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. Get fastq files from ENA using Run IDs. Contribute to B-UMMI/getSeqENA development by creating an account on GitHub.
29 Jan 2016 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using sys: connection failed while opening file within cryptographic module error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra27/SRR/ Probably it was running Python 3 but the authors expect Python 2. window.dll, 1 available version Warn when no FastQ files available from ENA · Issue #7 · ewels/sra-explorer · GitHub Download sra files no download windows 7 The command line tool historically used to download public bioinformatics data from the Sequencing Read Archive (SRA) is fastq-dump. Fastq-dump was awesome when it was developed, until bioinformatics workflows became more parallelized… Contribute to lanagarmire/Ssrge development by creating an account on GitHub. Several scripts for basic bioinformatics data manipulation - gavieira/python_bioinfo Find hot data sets in your area (of research)! Contribute to NCBI-Hackathons/SRA_Tinder development by creating an account on GitHub. a snakemake pipeline to process ChIP-seq files from GEO or in-house - crazyhottommy/pyflow-ChIPseq
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 tools in python for Hichip pipeline. Contribute to ChenfuShi/tools_for_Hichip development by creating an account on GitHub. 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
The default download path is in your home directory ~/ncbi . For example, you can find the SRA file SRR390728.sra in ~/ncbi/sra and the resource files in
GitHub Gist: star and fork hiraksarkar's gists by creating an account on GitHub. Youtubed l - Free download as Text File (.txt), PDF File (.pdf) or read online for free. Youtube dl Download the sra files for all GSMs from GEO website using aspc from Aspera or wget (in case when aspc fails). aspc and wget use different urls which are linked to copies of the same file. Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA). - ktmeaton/NCBImeta Contribute to MWJMerkx/pcfb_project development by creating an account on GitHub.