Wenchao Lin's repositories
AdaptorFinder
tools that finds adaptor unremoved subreads
AlignGraph
Algorithm for secondary de novo genome assembly guided by closely related references
annot-nf
Eukaryotic genome annotation pipeline implemented in Nextflow
BarcodeAnalysis
A python library of tools and prototypes for analyzing barcoded PacBio barcode data
cDNA_primer
Scripts for processing PacBio transcriptome (Iso-Seq) data
CEGMA_v2
The final version 2 release of our software to detect core genes in eukaryotic genomes
d3-cloud
Create word clouds in JavaScript.
DALIGNER-extras
Support for running DALIGNER (mostly scripts)
delftrnaseq
RNA-Seq pipeline used at the Delft Bioinformatics Lab
draw_ngs
Programs for drawing chromosome figure by using NGS data
ensembl-pipeline
Job management for the Ensembl Genebuild pipeline
fastStructure
A variational framework for inferring population structure from SNP genotype data.
fqBaseSum
This is a simple tool to calculate reads number and total base count in FASTQ file.
HlaTools
A series of tools and pipelines for genotyping MHC / HLA genes and alleles using SMRT Sequencing
MatchAnnot
Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
orthomcl-pipeline
Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/
PacBio-utilities
Collection of utilities for working with PacBio-based assemblies
PBHomer
Pacbio's homer scripts collection
pdom-genome-project
Polistes dominula genome project, a collaboration between the Insect Sociogenomics Lab at Iowa State University and the Computational Genome Science Lab at Indiana University
prokka
Rapid prokaryotic genome annotation
quota-alignment
Guided synteny alignment between duplicated genomes (within specified quota constraint)
readfq
A simple tool to calculate reads number and total base count in FASTQ file
RPI.PIHome2.0-GUI-Frontend
PiHome 2.0 is a RaspberryPI home automation open source project
scaffold_summary
A simple program for evaluate the assembly of a give genome.
walt
WALT is a read mapping program for bisulfite sequencing DNA methylation studies.