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
KMC modified to compute FMH sketches (hopefully)
kRISP-mER
A tool to generate personalized guide RNAs for CRISPR without using a reference genome
likelihood-of-mutated-protein
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.
mahmudhera's Repositories
mahmudhera/kegg-ko-annotation
mahmudhera/python_multiprocessing_example
Example of python multiprocessing with shared global data and return queue for future references
mahmudhera/kripmer_experiments_rerun
mahmudhera/FunUniFrac
mahmudhera/cami_ani_binning
Using ani calculated using FracMinHash, this repository will assign contigs to bins. Data collected from the CAMI website.
mahmudhera/sketch_refseq
commands to sketch all refseq genomes
mahmudhera/dn-ds-using-fracminhash
mahmudhera/snakemake-tutorial
A working knowledge on snakemake
mahmudhera/snakemake-sample
mahmudhera/2022-paper-protein-kmers
Forked from bluegenes
mahmudhera/visualize-graphs
mahmudhera/KEGG_data_extraction
mahmudhera/tsnnls
mahmudhera/likelihood-of-mutated-protein
mahmudhera/required-kmers-from-scale-factor
Computes the required number of kmers given a scale factor so that the resulting FracMinHash sketch does not have a large bias
mahmudhera/parse-gff
Parsing GFF file downloaded from GenBank database
mahmudhera/sourmash-ani-implementation-test
Testing if sourmash ani implementation returns correct values
mahmudhera/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.
mahmudhera/sourmash-wrapper-for-ani
Wrapper python scripts to compute any using sourmash
mahmudhera/mutate-genome-using-SMM
Mutate genome using the simple mutation model
mahmudhera/guidescan-cli
A gRNA database generation tool.
mahmudhera/gtdb-read-and-extract
Manually downloaded the .tree file from GTDB. Using bacteria tree. Then, starting with a random species, selected genomes that are at the same species, family, genus, order, phylum etc. Then, extracted pairwise distances from the entire taxonomy tree, and then computed tree off of those pairwise distances using neighbor joining.
mahmudhera/phylogenetic-tree
Very short repo that will construct and show a phylogenetic tree from pairwise distance matrix.
mahmudhera/ScaledMinHashFiles
All updates and files here
mahmudhera/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
mahmudhera/msc-code-and-figures
mahmudhera/linear-regression-matlab
mahmudhera/scaled-minhash-large-metagenome-expt
mahmudhera/pairwise-ani-calculation
mahmudhera/scaled-minhash-experiment-two-genomes