"That's a beautiful collection of public data you have here, it would be a shame if someone made it searchable." -- paraphrased
This repo provides examples that use sourmash to build FracMinHash sketches and search ~485,000 public metagenomes in the SRA with them in real time, using mastiff .
Quickstart - Jupyter Notebook
Click on the binder button below, and then select "Run... Run all cells", or hit the fast-forward button.
Quickstart - snakemake
Deposit sequences of interest in
sequences/
. Then run:
snakemake -j 1 --use-conda
and look in
mastiff_out/
.
Code Snippets
15 16 17 18 | shell: """ sourmash sketch dna -p k=21,noabund,scaled=1000 {input} \ --name-from-first -o {output} """ |
25 26 27 28 | shell: """ curl -H "Content-Type: application/json" --data-binary \ @{input} https://mastiff.sourmash.bio/search -o {output} """ |
Support
Do you know this workflow well? If so, you can
request seller status , and start supporting this workflow.
- Share:
-
-
-
Created: 1yr ago
Updated: 1yr ago
Maitainers:
public
URL:
https://github.com/sourmash-bio/2022-search-sra-with-mastiff
Name:
2022-search-sra-with-mastiff
Version:
1
Downloaded:
0
Copyright:
Public Domain
License:
BSD 3-Clause "New" or "Revised" License
Keywords:
- Future updates
Related Workflows
ENCODE pipeline for histone marks developed for the psychENCODE project
psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project.
The o...
Near-real time tracking of SARS-CoV-2 in Connecticut
Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
snakemake workflow to run cellranger on a given bucket using gke.
A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
ATLAS - Three commands to start analyzing your metagenome data
Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads
Genome assembly
Annotation track
checkm2
gunc
prodigal
snakemake-wrapper-utils
MEGAHIT
Atlas
BBMap
Biopython
BioRuby
Bwa-mem2
cd-hit
CheckM
DAS
Diamond
eggNOG-mapper v2
MetaBAT 2
Minimap2
MMseqs
MultiQC
Pandas
Picard
pyfastx
SAMtools
SemiBin
Snakemake
SPAdes
SqueezeMeta
TADpole
VAMB
CONCOCT
ete3
gtdbtk
h5py
networkx
numpy
plotly
psutil
utils
metagenomics
RNA-seq workflow using STAR and DESeq2
This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
This Snakemake pipeline implements the GATK best-practices workflow
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...