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atria

An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.

bamqc

Mapped QC analysis program

bin

Blurry Video Frame Interpolation (CVPR20)

bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

chloe

cp-hap

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

deepsimulator

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

fastp

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

flye

De novo assembler for single molecule sequencing reads using repeat graphs

gwas_problem

jellyfish

A fast multi-threaded k-mer counter

lightgraphsextras.jl

Additional functionality for LightGraphs.jl

masurca

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

multitrans

plotsr

Tool to plot synteny and structural rearrangements between genomes

principles-of-botanic-collections-value

rnaquast

Quality assessment of de novo transcriptome assemblies from RNA-Seq data

rosalind-club

Bioinformatics Rosalind Problems solved by members of the Rosalind Club at Skoltech. 2022

sangtk

SangTK is an ML-backed toolkit that improves the quality of Sanger base calls.

scripts-on-genomics

Scripts for some simple jobs in Bioinformatics.

sleuth

Differential analysis of RNA-Seq

soapdenovo-trans

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.

tabbed_txt_rows_filter

Script to filter rows in tabbed txt files such as logfiles or sequencing summary, by another tabbed txt

transabyss

de novo assembly of RNA-seq data using ABySS

vcf-annotator

Add biological annotations to variants in a given VCF file.

xmatchview

🗻 Visualization of genome/gene sequence synteny

zotero2md

A Python library to retrieve annotations and notes from Zotero and save them into Markdown files.