Software Updates

GATK

(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.

Luna

is an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.

RBPBench

RBPBench is multi-function tool to evaluate CLIP-seq and other genomic region data using a comprehensive collection of known RNA-binding protein (RBP) binding motifs.

DNAscent

DNAscent is software designed to detect the base analogues BrdU and EdU in single molecules of DNA sequenced on the Oxford Nanopore platform

gsMap

gsMap (genetically informed spatial mapping of cells for complex traits) integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including diseases, in a spatially resolved manner.

strobealign

a read mapper that is typically significantly faster than other read mappers while achieving comparable or better accuracy, see the performance evaluation.

LazyPredict

Lazy Predict helps build a lot of basic models without much code and helps understand which models works better without any parameter tuning.

tidk

Identify and find telomeres, or telomeric repeats in a genome.

LongReadSum

LongReadSum supports FASTA, FASTQ, BAM, FAST5, and sequencing_summary.txt file formats for quick generation of QC data in HTML and text format.

smoothxg

Local reconstruction of variation graphs using partial order alignment. Pangenome graphs built from raw sets of alignments may have complex local structures generated by common patterns of genome variation. smoothxg can be used to extract the consensus pangenome graph by applying the heaviest bundle algorithm to each chain.

falco

is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.

Recentrifuge

Robust comparative analysis and contamination removal for metagenomics

epic2

Ultraperformant Chip-Seq broad domain finder based on SICER.

hifiasm_meta

Metagenome assembler for Hifi reads, based on hifiasm.

panacus

a counting tool for pangenome graphs. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.

gappa

Genesis Applications for Phylogenetic Placement Analysis

VeryFastTree

a new tool designed for efficient phylogenetic tree inference, specifically tailored to handle massive taxonomic datasets. It is a highly-tuned implementation based on the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments.

Spark

a multi-language engine for executing data engineering, data science, and machine learning on single-node machines or clusters.

covtobed

a tool to generate BED coverage tracks from BAM files. It reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range.

EPA-ng

a complete rewrite of the Evolutionary Placement Algorithm (EPA), previously implemented in RAxML. It uses libpll and pll-modules to perform maximum likelihood-based phylogenetic placement of genetic sequences on a user-supplied reference tree and alignment.