tahashmi

ArrowSAM

Genomics datastructures using Apache Arrow

variant-calling-at-scale

Scalable and High Performance Variant Calling on Cluster Environments

hapcorrect

Haplotypes phase-switching errors correction in long reads

Wakhan

Haplotype-specific somatic copy number aberrations/profiling from long reads sequencing data

arrow

Apache Arrow is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. It also provides computational libraries and zero-copy streaming messaging and interprocess communication. Languages currently supported include C, C++, Java, JavaScript, Python, and Ruby.

lab1

Advanced Computing Systems Lab1 files

tahashmi/lab1

Advanced Computing Systems Lab1 files

tahashmi/arrow

Apache Arrow is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. It also provides computational libraries and zero-copy streaming messaging and interprocess communication. Languages currently supported include C, C++, Java, JavaScript, Python, and Ruby.

tahashmi/riscv-wiki

tahashmi/arrow-datafusion

Apache Arrow DataFusion and Ballista query engines

tahashmi/bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

tahashmi/cglib-conv

tahashmi/cpplinks

A categorized list of C++ resources.

tahashmi/custom-images

Tools for creating Dataproc custom images

tahashmi/deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

tahashmi/dotfiles

Repository to keep (dot files) settings in a linux system

tahashmi/fletcher

Fletcher: A framework to integrate FPGA accelerators with Apache Arrow

tahashmi/GMM-EM-Python

Python implementation of EM algorithm for GMM. And visualization for 2D case.

tahashmi/hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

tahashmi/mark-duplicates

Mark PCR duplicates and sequencing platform / optical duplicates in single-end SAM files

tahashmi/Matplotlib-Python-Graphs

A small effort to build a simple library to generate different types of graphs in Python.

tahashmi/matplotlib-tutorial

Matplotlib tutorial for beginner

tahashmi/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

tahashmi/MPI_RMA

tahashmi/mpiMarkDup

mpi and C based marking of duplicates for Next Generation Sequencing technology

tahashmi/parallel-merge-sort

Shared Memory, Message Passing, and Hybrid Merge Sort: UPC, OpenMP, MPI and Hybrid Implementations

tahashmi/planets

This is all about Planet

tahashmi/sarviewer

Generate graphs with gnuplot or matplotlib (Python) from sar data

tahashmi/softiwarp

SoftiWARP: Software iWARP kernel driver and user library for Linux

tahashmi/SparkGA1

SparkGA is an Apache Spark based scalable implementation of the best practice DNA analysis pipeline by Broad Institute.

tahashmi/SparkGA2

tahashmi/vector_addition_tutorials

This repository stores all of the OLCF vector addition tutorials