ctb

#! /usr/bin/env python
"""
Usage:

python -m screed db <sequencefile>
python extract-screed.py <list of names> <sequencefile>
"""
import argparse, screed, sys

def main():

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subtract

Subtract signatures from each other

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Simple demonstration code to load sequences, compute signature, and do a search against an SBT.

sourmash compute --scaled 10000 -f data/GCF*.fna.gz
sourmash index -k 31 test.sbt GCF*.sig

./build-and-search.py test.sbt data/GCF_000005845.2_ASM584v2_genomic.fna.gz

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banded kraken - example usage

Prepare the database:

mkdir ecoli_many_sigs
cd ecoli_many_sigs
curl -O -L https://github.com/dib-lab/sourmash/raw/master/data/eschericia-sigs.tar.gz
tar xzf eschericia-sigs.tar.gz
cd ../

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*~
*.pyc
.sbt.delmont31/
.sbt.subs1/
.sbt.subs2/
.sbt.tully31/
delmont-genome-sigs.tar.gz
delmont-genome-sigs/
delmont31.sbt.json
subs1.sbt.json

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reverse indexing foo for sourmash signatures

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foo!

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Some scripts for parsing NCBI taxonomy information => sourmash.

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multik analysis of strain variation

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Benchmarking k-mer load times against RAM

see hashsize_bench.ipynb