Software Updates

selscan

a program to calculate EHH-based scans for positive selection in genomes.

TideHunter

efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain.

Crumble

controllable lossy compression of BAM/CRAM files.

pybedtools

pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.

Dextractor

bax file decoder and data compressor.

RAxML-NG

a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.

TreeBeST

(Tree Building guided by Species Tree) is a versatile program that builds, manipulates and displays phylogenetic trees.

downpore

a suite of tools for use in genome assembly and consensus.

fqtools

an efficient FASTQ manipulation suite.

FastME

FastME provides distance algorithms to infer phylogenies.

fastq-scan

fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format.

abPOA

an extended version of Partial Order Alignment (POA) that performs adaptive banded dynamic programming (DP) with an SIMD implementation.

srprism

Short Read Alignment Tool

HULK

(Histosketching Using Little Kmers) a tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.

SKESA

(Strategic Kmer Extension for Scrupulous Assemblies) a de-novo sequence read assembler for microbial genomes.

TN93

a fast distance calculator that computes pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.

FastANI

developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).

OCOCO

the first program capable of inferring variants in a real-time, as read alignments are fed in. Ococo inputs unsorted alignments from a stream and infers single-nucleotide variants, together with a genomic consensus, using statistics stored in compact several-bit counters.

PRANK

a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.

daligner

finds all significant local alignments between reads.

scrm

a coalescent simulator for biological sequences.

CLARK

fast, accurate and versatile k-mer based classification system.

Lighter

a kmer-based error correction method for whole genome sequencing data.

SNP-sites

rapidly extracts SNPs from a multi-FASTA alignment.

Longshot

a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).

RNA-SeQC

fast, efficient RNA-Seq metrics for quality control and process optimization.

kallisto

a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

Tracy

basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files.

Filtlong

a tool for filtering long reads by quality.

Cuttlefish

a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s).

UShER

a program that rapidly places new samples onto an existing phylogeny using maximum parsimony. It is particularly helpful in understanding the relationships of newly sequenced SARS-CoV-2 genomes with each other and with previously sequenced genomes in a global phylogeny.

Subread

comprises a suite of software programs for processing next-gen sequencing read data including

- Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
- Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well.
- featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins.
- Sublong: a long-read aligner that is designed based on seed-and-vote.
- exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

UMI-tools

tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Salmon

a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses algorithms to provide very quick, accurate expression estimates using little memory and performs inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.