Wouter De Coster (@wdecoster)
github

wdecoster

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Top repositories

1

NanoPlot

Plotting scripts for long read sequencing data
Python
430
star
2

nanopack

An overview of all nanopack tools
Python
210
star
3

nanofilt

Filtering and trimming of long read sequencing data
Python
189
star
4

chopper

Rust
150
star
5

cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
Rust
127
star
6

nanocomp

Comparison of multiple long read datasets
Python
103
star
7

nanostat

Create statistic summary of an Oxford Nanopore read dataset
Python
92
star
8

nanoQC

Quality control tools for nanopore sequencing data
Python
91
star
9

methplotlib

Plotting tools for nanopore methylation data
Python
90
star
10

nano-snakemake

A snakemake pipeline for SV analysis from nanopore genome sequencing
Python
51
star
11

nanolyse

Remove lambda phage reads from a fastq file
Python
28
star
12

surpyvor

A python wrapper around SURVIVOR
Python
19
star
13

kyber

Rust
17
star
14

DEA.R

Script to automate differential expression analysis using DESeq2, edgeR or limma-voom
R
17
star
15

phasius

Rust
13
star
16

nanoget

Functions to extract information from Oxford Nanopore sequencing data and alignments
Python
11
star
17

nanomath

A few simple math function for other Oxford Nanopore processing scripts
Python
9
star
18

PromisingPreprint

A python twitter bot tweeting about preprints reaching an interesting altmetric score
Python
8
star
19

STRdust

Tandem repeat genotyping from long reads
Rust
8
star
20

enrichr_cli

Python script to use enrichr from command line (http://amp.pharm.mssm.edu/Enrichr/)
Python
7
star
21

nanotest

Small test datasets for testing nanopack scripts and modules
Shell
5
star
22

make_arrow

A Rust tool to create an arrow file from a cram/bam file
Rust
4
star
23

pathSTR

Repository with code for the analysis of pathogenic STRs in the 1000G ONT resequencing data
Jupyter Notebook
4
star
24

read_length_SV_discovery

Jupyter Notebook
3
star
25

nanoplotter

Plotting functions of Oxford Nanopore sequencing data
Python
2
star
26

fast5purge

Purge a fast5 file from sensitive information
Python
2
star
27

tool-packaging

Some notes on how to make a pypi package
Python
1
star
28

GermlineCNVCaller

Testing the GATK4.beta.5 GermlineCNVCaller
Python
1
star
29

nanosplit

Splitting Oxford Nanopore data in a fail and pass dataset using a user defined quality cutoff
Python
1
star
30

determine-gender

Scripts to determine the gender of samples in exome and transcriptome sequencing
Python
1
star
31

combine_images

Bit of Python code to resize and combine images
Python
1
star