Software Updates

deepTools

a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

Snakemake

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

DIAMOND

a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.

corset

Software for clustering de novo assembled transcripts and counting overlapping reads.

R-pkgs-Biogrids

contains common and requested R packages for BIOGRIDS. This title is dependent on R.

R

a free software environment for statistical computing and graphics.

spaceranger

Visium Spatial Software Suite for analyzing and visualizing spatial gene and protein expression data

EMA

Fast & accurate alignment of barcoded short-reads

lastz

LASTZ is a program for aligning DNA sequences, a pairwise aligner.

vcf2parquet

Convert a vcf in parquet.

isoseq3

Scalable De Novo Isoform Discovery

PFP

Tool to build the parse and the dictionary for VCF files using the approach described in Prefix-Free Parsing for Building Big BWTs

KMCP

accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

abismal

abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads

msamtools

microbiome-related extension to samtools

LevioSAM2

Fast and accurate coordinate conversion between assemblies

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.

STAR

(Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.

sdm

simple demultiplex tool for FASTQ demultiplexing and dereplication.

platon

Plasmid contig classification and characterization for short read draft assemblies.

InSilicoSeq

A sequencing simulator.

dnmtools

a set of tools for analyzing DNA methylation data from bisulfite sequencing

AGAT

(Another Gff Analysis Toolkit) a suite of tools to handle gene annotations in any GTF/GFF format.