Sequencing Tools

BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.

CryptoGenotyper is a bioinformatics tool for rapid Cryptosporidium identification. The CryptoGenotyper is a fast and reproducible tool that can be used to classify the genotype of Cryptosporidium samples by directly analyzing the DNA electropherogram files that correspond to two of its characteristic gene markers: SSU rRNA and gp60.

R library that performs differential analysis for count-based sequencing data. It detects differentially expressed genes (DEGs) from RNA-seq and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). Its core is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

Peak finder for NGS datasets that can integrate replicates and assign peak boundaries accurately.

Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences

A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.

OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.

Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.

Aligns and optionally taxonomically classifies your rRNA gene sequences. Reference based multiple sequence alignment

A program for assemblying short DNA sequences. The program cycles through sequence data stored in a hash table and progressively searches through a prefix tree for the longest possible k-mer between any two sequencis.

An algorithm for structural variation detection from third generation sequencing alignment.

Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.

TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.

A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.

VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files. VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads and better scalability than many Java based variant callers.

VarScan, an open source tool for variant detection that is compatible with several short read align-ers.

Variant tool set that discovers short variants from Next Generation Sequencing data.

Atropos is tool for specific, sensitive, and speedy trimming of NGS reads.

BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.

Tools for early stage NGS alignment file processing including fast sorting and duplicate marking.

Collaborative project to facilitate the interconversion of life science data from one format to another.

Software for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error.

Bowtie is an ultrafast, memory-efficient short read aligner.

breseq is a computational pipeline for finding mutations relative to a reference sequence using high-throughput DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.

Cluster a nucleotide dataset into representative sequences.

Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.

clearCNV is a bioinformatics software package designed to detect Copy Number Variations (CNVs) in targeted Next-Generation Sequencing (NGS) panel data. It is specifically built to handle ambiguity and noise, making it effective at identifying larger multi-exon CNVs that might otherwise be missed.

Suite of tools to discover structural variations such as (larger) insertions and deletions in genomes from paired-end sequencing reads.

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis

Deciphering the exact breakpoints of structural variations using long sequencing reads.

Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.