Pinned Repositories
fmh-funprofiler
A functional profiler for metagenomes using FracMinHash
mutation-rate-ci-calculator
This software calculates a confidence interval for the mutation rate from a set of observed containment indices under a simple nucleotide mutation process.
YACHT
A mathematically characterized hypothesis test for organism presence/absence in a metagenome
dist-sim-metrics-using-fmh
Compute different metrics using FMH, and also without using sketch, and see the results
dn-ds-using-fracminhash
fancy-mutation-model
A "non-simple" mutation model supporting insertion, deletion and substitutions
frac-kmc
Fast FracMinHash sketch generator
kRISP-mER
A tool to generate personalized guide RNAs for CRISPR without using a reference genome
phylogenetic-tree-using-fracminhash
This repo can be thought of as a counterpart to Mashtree - which computes a tree based off of Mash distance. Instead, in this repo, we build a tree based off of FracMinHash distance.
qual-exams
mahmudhera's Repositories
mahmudhera/qual-exams
mahmudhera/fancy-mutation-model
A "non-simple" mutation model supporting insertion, deletion and substitutions
mahmudhera/frac-kmc
Fast FracMinHash sketch generator
mahmudhera/accelarated_sketch_comparison
Investigation of GPU acceleration in many-to-many sketch comparison
mahmudhera/afsampling
Investigating cardinality of sketch sizes when sketching is done using affirmative sampling
mahmudhera/annotate_genomes_with_ncbi_taxid
mahmudhera/capnproto_example
In this repo, we will write a file in binary using capnproto
mahmudhera/compare_fmh_simka_mash
Compare FracMinHash, SIMKA, and Mash in computing pairwise distances for a number of genomes/metagenomes etc.
mahmudhera/compare_genome_sketches
mahmudhera/compare_ground_truths
mahmudhera/cpp_md5sum
Implement md5sum in a C++ project
mahmudhera/cpp_mmh3
mahmudhera/dnds_for_individual_genes
A test if our estimator for dN/dS (or Ka/Ks) works for individual genes
mahmudhera/docker_demo
In this repo, I will create a web application to run in docker. An attempt to gain working knowledge in docker
mahmudhera/fast_yacht_train
This repository implements a faster version of yacht train
mahmudhera/fastgather_benchmark
mahmudhera/find_scale_factor_cosine_fmh
Find an appropriate scale factor for estimating cosine similarity using FracMinHash sketch
mahmudhera/fmm
Fancy mut model
mahmudhera/KEGG-sketch-each-KO
KEGG sketching and functional annotation using the "sketch each KO" approach
mahmudhera/KEGG_sketching_annotation
Scripts to sketch KEGG and explore using FracMinHash as a way to functionally annotate a metagenome
mahmudhera/krispmer-expreminets
Codes of all experiments to prepare results are in this repository, along with comments
mahmudhera/nextflow_demo
In this repo, we will do a task using nextflow. This is a trial project for myself, to get familiar with nextflow so I have a working understanding of the basics.
mahmudhera/parse_nominations
mahmudhera/process_sam_bam
mahmudhera/profile_processes
Monitor cpu time, peak and average memory usage of processes belonging to a user
mahmudhera/run_camisim
Python wrapper to run camisim simulations. To be used in the "fast accurate metagenomic functional profiler" project
mahmudhera/similarity_analysis_of_metageomes
mahmudhera/sourmash_alternate_implementations
Implement sourmash functionalities in cpp to investigate potential speedups
mahmudhera/test_cpp_code
In this repo, I test small cpp code segments
mahmudhera/YACHT
A rigorous hypothesis test for organism presence/absence in a metagenome