GitHub profile: https://github.com/shubhamchandak94/

This page lists some of the open-source software tools I have contributed to. Almost all the tools have permissive licenses and we welcome their adoption and modification for various applications. Please refer to the corresponding websites to find out more details about the software including contributors, publications, usage details etc. The page also highlights some projects by others which might be of interest to the broader research community. Such projects are marked accordingly.

Genomic data compression

  • SPRING: compressor for genomic sequencing reads in FASTQ files
    [GitHub]

  • Lossy compression evaluation for nanopore raw signal data
    [GitHub]

  • NanoSpring: reference-free lossless compression of nanopore sequencing reads
    [GitHub]
    Developed together with Qingxi Meng and Yifan Zhu

  • Genie: open source MPEG-G codec for genomic data representation
    [GitHub]
    Work done as part of the Genie team

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General-purpose data compression

  • Stanford Compression Library
    [GitHub]
    In collaboration with Kedar Tatwawadi and Pulkit Tandon

  • LFZip: Lossy compressor for multivariate floating-point time series
    [GitHub]
    Work done in collaboration with Siemens

  • DZip: General-purpose lossless compression based on novel neural network modeling
    [GitHub]
    Lead contributor: Mohit Goyal

  • DeepZip: Lossless Data Compression using Recurrent Neural Networks
    [GitHub]
    Lead contributor: Mohit Goyal

  • BSC: high performance lossless compressor based on BWT
    [GitHub]
    Fork of work by Ilya Grebnov

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DNA storage

  • LDPC DNA storage library for Illumina sequencing based DNA storage.
    [GitHub]

  • Convolutional coding based DNA storage for nanopore sequencing
    [GitHub]

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Error correction coding

  • ProtographLDPC: Implementation of Protograph LDPC codes
    [GitHub] [Website]
    Lead contributor: Roshan Prabhakar

  • VT codes for single insertion/deletion errors for general alphabet
    [GitHub]

  • Single edit correcting code for quaternary alphabet
    [GitHub]
    Fork of work by Daniel Tan done as part of EE 276: Information Theory

  • LDPC-codes: library for generation and application of LDPC codes
    [GitHub] [Website]
    Fork of work by Radford Neal

  • Stabilizer codes for quantum error correction
    [GitHub]
    Work done as part of course project for CS 269Q

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Miscellaneous

  • Template Python Server
    [GitHub]

  • Pose animator streaming: twist on the conventional video streaming pipeline for reducing bandwidth and latency
    [GitHub] [Blog]
    Mentored as part of the STEM to SHTEM 2020 internship for high schoolers

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