Skip to content
Output trusted regions from raw sequencing data.
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
test-data
.gitignore
.travis.yml
README.md
requirements.txt
setup.py
syrah
test_syrah.py

README.md

syrah!

syrah reads sequences from stdin and outputs subsequences containing solid or trusted k-mers suitable for counting or MinHashing.

syrah automatically exits when it has seen enough solid k-mers.

Options

You can specify the number of solid k-mers with -n.

You can set the k-mer size with -k.

You can eliminate all output with -q.

There are no other options because options lead to anger. Anger leads to hate. Hate leads to suffering.

Use cases

The primary use case for the moment is to extract a subset of solid k-mers for loading into sourmash signatures. For example,

dump-fastq -A $SRA_ID -Z | syrah | sourmash compute - -o out.sig

will extract the first 1m solid k-mers from the given SRA data set and feed them into sourmash to compute a signature. Once enough k-mers are found, syrah will terminate the stream.

The default parameters are designed for small microbial genomes (where 1m k-mers is usually between 20-50% of the genome) and may be OK for metagenome and transcriptome overlap analysis, but for other situations you may need to vary -n.

CTB 12/2016

You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.