Skip to main content

Sequence Idenification using Decision tRees; a tool to classify DNA reads using machine learning models.

Project description

SIDR (pronounced: cider) is a tool to filter Next Generation Sequencing (NGS) data based on a chosen target organism. SIDR uses data fron BLAST (or similar classifiers) to train a decision tree model to classify sequence data as either belonging to the target organism, or belonging to something else. This classification can be used to filter the data for later assembly.

Note: SIDR is alpha software. Features are currently incomplete and subject to major change.


To install SIDR, clone this repository and run, or use pip to install.

pip install sidr

See the documentation for more details.


SIDR has two main modes. Default mode takes several bioinformatics files as input, and computes a decision tree based on percentage GC content and per-base sequencing coverage. To run it, use:

sidr default -d [taxdump path] -b [bamfile] -f [assembly FASTA] -r [BLAST results] -k tokeep.contigids -x toremove.contigids -t [target phylum]

Runfile mode takes a tab-delimited file of contigs, variables, and classification as input. To run it, use:

sidr runfile -i [runfile] -k tokeep.contigids -x toremove.contigids -t [target phylum]

See the documentation for more details.


  • More complete documentation
  • More unit tests

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for SIDR, version 0.0.2a2
Filename, size File type Python version Upload date Hashes
Filename, size SIDR-0.0.2a2-py2.py3-none-any.whl (13.7 kB) File type Wheel Python version py2.py3 Upload date Hashes View hashes
Filename, size SIDR-0.0.2a2.tar.gz (20.4 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page