Jianshu_Zhao's repositories
vsearch
Versatile open-source tool for metagenomics
ampvis2
Tools for visualising amplicon data
hyperminhash
HyperMinHash: Bringing intersections to HyperLogLog
Stegen_etal_ISME_2013
Code for running analyses carried out in Stegen et al. 2013, ISME
micronota
annotation pipeline for microbial genomes and metagenomes
pytorch_experiments
Auto Encoders in PyTorch
blast2ani
Garcia, S. L., Stevens, S. L. R., Crary, B., Martinez-Garcia, M., Stepanauskas, R., Woyke, T., Tringe, S. G., Andersson, S., Bertilsson, Malmstrom, R. R., McMahon, K. D. (ISMEJ). Genome level exploration of abundant and uncultivated freshwater bacteria reveals distinct and dynamic populations.
bernstein-2016-productivity-and-diversity
🦠 📓 A microbiome paper in ISME
swarm
A robust and fast clustering method for amplicon-based studies
gattaca-public
Lightweight metagenomic binning
BanfieldLabProjects
An index describing the public and private repositories that Banfield lab members can request access to.
mcrm
microbial consumer resource model
libfast_knn
C++ library of k-nearest neighbors algorithm (k-NN), faster because uses Armadillo lib
python-Levenshtein
The Levenshtein Python C extension module contains functions for fast computation of Levenshtein distance and string similarity
ezTree
A Perl pipeline for identifying marker genes and build phylogenetic trees for a set of genomes
taxadiva
TAXonomy Assignment and DIVersity Assessment - wrapper script for facilitating analysis of nifH amplicon sequences
shotmap
A Shotgun Metagenome Annotation Pipeline
RAMBL
Large-scale 16S gene assembly using metagenomic shotgun sequences
k-nearest-neighbors
A Simple k-nearest neighbors implementation in C++
katome
De novo genome assembler based on De Bruijn graph
metakallisto
Using kallisto for metagenomic analysis
sad-comparison
Elita Baldridge's dissertation repository
macroecotools
Tools for Macroecological Analyses Using Python
COMPARE
compare
parasailors
Rust bindings to parasail, a SIMD-accelerated pairwise sequence alignment library.
akutils-v1.1.1
Mostly useful scripts and files for processing MiSeq amplicon data
co-occurrence_python
I've been having some issues with slow R...trying this out in python