JinfengChen

biocode

Bioinformatics code libraries and scripts

Transposition_new

10x

bionano

maffilter

The MafFilter genome alignment processor

mafTools

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

maize_v4_TE_annotation

scripts and intermediate files used to annotate TEs in Jiao et al.

pacbio_variant_caller

SMRT-SV: Structural variant and indel caller for PacBio reads

pop_analysis

PythonNGSTools

Scripts for NGS processing

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116

Rice_pop

RILs_Preparation

arcs

Scaffold genome sequence assemblies using 10x Genomics data

Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

CNVRepeat

CNVRepeat_eva

deeplearning-biology

A list of deep learning implementations in biology

gdc

Short scripts for converting genetic data between formats.

HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

HomolContigsByAnnotation

python script to identify genes that are present on multiple contigs

jekyll

:globe_with_meridians: Jekyll is a blog-aware, static site generator in Ruby

mlift

A mummer based genomic coordinate liftover tool

NGS_data_processing

Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.

Pacbio

PacBio-utilities

Collection of utilities for working with PacBio-based assemblies

QTL_pipe

SURVIVOR

Toolset for SV simulation, comparison and filtering

svmu

A program to call variants from genome alignment

xpclr

Code to compute the XP-CLR statistic to infer natural selection