Smith Lab

A computational biology research group at USC

Overview
Repositories
Projects
Packages
People

README.md

smithlabcode

This organization is for code produced as a byproduct of our research in computational biology. All our repos can be found here. Our reseaerch covers diverse topics in computational genomics. So our code covers diverse topics. If you have any questions, here are several options:

Post your question as an issue in the corresponding repo.
Email the author of the code (which in most cases includes myself, Andrew).
Email me. My address is in my profile.

We release our code so it might help you. If it's not working properly or optimally, please ask us and we'll do our best to make it work for you.

Pinned Loading

methbase methbase Public

Thousands of high-quality analyzed methylomes.

1
preseq preseq Public

Software for predicting library complexity and genome coverage in high-throughput sequencing.

C++ 97 17
falco falco Public

A tool to assess the quality of sequence read data

C++ 138 13
ribotricer ribotricer Public

A tool for accurately detecting actively translating ORFs from Ribo-seq data

Python 43 10
abismal abismal Public

Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

C++ 20 6
dnmtools dnmtools Public

Tools for analyzing DNA methylation data

C++ 47 11

Repositories

Type Language Sort

falco Public
A tool to assess the quality of sequence read data

smithlabcode/falco's past year of commit activity

C++ 138 MIT 13 12 (1 issue needs help) 1 Updated Aug 28, 2026
preseq Public
Software for predicting library complexity and genome coverage in high-throughput sequencing.

smithlabcode/preseq's past year of commit activity

C++ 97 GPL-3.0 17 18 1 Updated Aug 26, 2026
preseqR Public
An R package for estimating library complexity

smithlabcode/preseqR's past year of commit activity

R 13 4 7 0 Updated Aug 25, 2026
methbase Public
Thousands of high-quality analyzed methylomes.

smithlabcode/methbase's past year of commit activity

1 MIT 0 0 0 Updated Aug 24, 2026
abismal Public
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

smithlabcode/abismal's past year of commit activity

C++ 20 GPL-3.0 6 2 0 Updated Aug 14, 2026
dnmtools Public
Tools for analyzing DNA methylation data

smithlabcode/dnmtools's past year of commit activity

C++ 47 GPL-3.0 11 31 (1 issue needs help) 0 Updated May 18, 2026
ribotricer Public
A tool for accurately detecting actively translating ORFs from Ribo-seq data

smithlabcode/ribotricer's past year of commit activity

Python 43 GPL-3.0 10 6 0 Updated Feb 14, 2026
smithlab_cpp Public
C++ code library that includes functions used in many of the Smith lab projects

smithlabcode/smithlab_cpp's past year of commit activity

C++ 4 5 12 0 Updated Jan 6, 2026
slsa-attester Public
SLSA Attester

smithlabcode/slsa-attester's past year of commit activity

0 MIT 0 0 0 Updated Dec 26, 2025
bamxx Public
HTSlib wrapper (mostly for BAM/SAM) in C++.

smithlabcode/bamxx's past year of commit activity

C++ 0 MIT 2 0 0 Updated Dec 17, 2025