amsyuan

amsyuan's Stars

• rrwick/Porechop

  adapter trimmer for Oxford Nanopore reads

  Language:C++347131

• rcs333/VAPiD

  VAPiD: Viral Annotation and Identification Pipeline

  Language:Shell5115

• BioInfoTools/BBMap

  (Not Offical) BBMap short read aligner, and other bioinformatic tools.

  Language:Java215111

• jenniferlu717/Bracken

  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

  Language:C++29750

• epi2me-labs/wf-metagenomics

  Metagenomic classification of long-read sequencing data

  Language:Python6623

• bioinformatics-centre/kaiju

  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

  Language:C27367

• jvolkening/b2b-utils

  Genomics utilities from BASE₂BIO

  Language:Perl2

• wdecoster/nanopack

  An overview of all nanopack tools

  Language:Python22416

• rrwick/Bacterial-genome-assemblies-with-multiplex-MinION-sequencing

  Language:Shell339

• rrwick/Filtlong

  quality filtering tool for long reads

  Language:C++30328

• wdecoster/NanoPlot

  Plotting scripts for long read sequencing data

  Language:Python44448

• a-slide/pycoQC

  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

  Language:Python27341

• CarolinaPB/nanopore-assembly

  Pipeline to assemble oxford nanopore long sequencing reads and perform variant calling with long and short reads

  Language:Python9

• amkram/shusher

  Private, browser-based placement of genome sequences on phylogenetic trees using UShER.

  Language:JavaScript101

• FelixKrueger/TrimGalore

  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

  Language:Perl479150

• acorg/ncbi-taxonomy-database

  How to make a mysql or sqlite database of NCBI taxonomy data for use with the dark-matter lineage fetcher

  Language:Shell72

• fbreitwieser/pavian

  🌈 Interactive analysis of metagenomics data

  Language:R40378

• soulteary/llama-docker-playground

  Quick Start LLaMA models with multiple methods, and fine-tune 7B/65B with One-Click.

  Language:Python35249

• microsoft/DeepSpeed

  DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.

  Language:Python36k4.2k

• meta-llama/llama

  Inference code for Llama models

  Language:Python57k9.6k

• juncongmoo/pyllama

  LLaMA: Open and Efficient Foundation Language Models

  Language:Python2.8k309

• agemagician/ProtTrans

  ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

  Language:Jupyter Notebook1.1k155

• bhattlab/MGEfinder

  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

  Language:Python11416

• macman123/track_structural_variants

  A set of scripts used for tracking structural variations around a gene of interest

  Language:R62

• anonymized-research/progen2

  Language:Python104

• xrsrke/progen

  Generating new proteins using language models

  Language:Jupyter Notebook4

• AnantharamanLab/PropagAtE

  Prophage Activity Estimator

  Language:Python263

• tseemann/shovill

  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

  Language:Perl21545

• apcamargo/genomad

  geNomad: Identification of mobile genetic elements

  Language:Python20119

• Rayin-saber/IAV-CNN

  A 2D convolutional neural network model to predict antigenic variants of influenza A virus through sequence data

  Language:Python84