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alternative-splicing-study-under-mineral-nutrient-deficiency

apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

ashr

An R package for adaptive shrinkage

assemblytics

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

atac-seq-pipeline

ATAC-seq analysis pipeline

bam-readcount

count DNA sequence reads in BAM files

bamscale

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

bat1k

Perl scripts used in Bat1K annotation for adding splice informative isoforms

bazam

A read extraction and realignment tool for next generation sequencing data

bio

General bioinformatics functions in Python

bioinformatic

bioinformatics-training

Bioinformatics training resources

broomcorn-millet-genome-assembly

Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

chinamap

cnspipeline

cp-hap

Estimate the ratio of different directions of single copy in the chloroplast genome

dash-bio

Open-source bioinformatics components for Dash

dbg2olc

The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

dcns

conserved non-coding sequence

deepsv

Calling deletions using deep convolutional neural

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

dinumt

dupgen_finder

A pipeline used to identify different modes of duplicated gene pairs

edta

Extensive de-novo TE Annotator

fasta36

Git repository for FASTA36 sequence comparison software

fastaq

Python3 scripts to manipulate FASTA and FASTQ files

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

find_cns

find conserved non-coding sequences (CNS)

flas

Fast and High Throughput Algorithm for PacBio Long Read Self-Correction

flye

Fast and accurate de novo assembler for single molecule sequencing reads