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There are few software that I have developed to help me with my work. Some have been so helpful, that I have made them available to other collegues for use. I hope you try few of these and possible give some feedback. Even better, use them in your work. 😃

Well documented, usable and efficient code is research made more accessible!

Bioinformatics Related Software

Notice Seq2CovVec (coverage vectorization program is being developed. Soon to be ready! check Github)


LRBinner

Accepted for presentation at WABI 2021. This work published at 10.4230/LIPIcs.WABI.2021.11

Code is available at Github.


MetaBCC-LR

MetaBCC-LR logo

This is the first long read binner that is 100% reference-free and to use both coverage and composition for binning.

This piece of work has been presented at ISMB 2020 and published in Bioinformatics.

Code is available at Github.


PlasLR

PlasLR logo

This tool facilitates extension of plasmid classification for long reads. Classification of plasmids before assembly of long reads have proven to improve quality of assembled plasmids and chromosomes.

Presented at GLBIO 2021

Code availalbe at Github


GraphPlas

GraphPlas logo

This tool enables improvement of plasmid classification of NGS assemblies using assembly graph.

Work has been presented at APBC 2021 published in IEEE TCBB

Code available at Github


Software for Machine Learning


Seq2Vec

Most Bioinformatics machine learning tasks rely on oligonucleotide frequency vectors. They were so frequently used in my work that I decided to make an efficient tool myself for the task. This helps me to re-use code in a highly modular fashion. Hope this will help someone else as well;

Code in Github


Object Annotation Maker

Object annotations for computer vision is a tedius task. However, more often we have object images with white backgrounds. In this tool; you get to pick object images and desired backgrounds for image generation. There are many parameters that one can use to generate a large dataset of images for computer vision tasks.

Read the blog in Medium

Code in Github


Other Useful Software/Libraries I have made


Smart Clock (Using M5 Stick C Plus)

drawing Reference image from Github

This is a small hobby project where I built a small clock using M5 Stick C Plus which is a cute little WiFi enabled IOT device.

Code in Github

MQTT Door Sensor

A power efficient, fast and response door sensor implementation that is 100% compatible with Home Assistant. This is essentially a template and can be edited at will to derive a completely different Home Assistant compatible IOT device.

Code in Github

AWS Lambda Boilerplate

A simple, robus and lightweight boilerplate that is highly extensible in large scale AWS lambda projects. This has proven success in Vinyl.LK which is an online catalogue of Sri Lankan vinyl records.

Read the blog in Medium

Code in Github