Software Updates

WhatsHap

a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.

fastp

is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

geofetch

Downloads data and metadata from GEO and SRA and creates standard PEPs.

pomoxis

Assembly, consensensus, and analysis tools by ONT research

DERNA

RNA sequence design for a target protein sequence

DeepLC

Retention time prediction for (modified) peptides using Deep Learning.

PhiSpy

Prophage finder using multiple metrics

alevin-fry

is a tool for the efficient processing of single-cell data based on RAD files produced by alevin.

simpleaf

simpleaf is a rust framework to make using alevin-fry even simpler.

glimpse-bio

GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.

leafcutter

Leafcutter quantifies RNA splicing variation using short-read RNA-seq data.

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.

MMseqs2

an ultra fast and sensitive sequence search and clustering suite

Julia

is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.

Cutadapt

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

rnashapes

RNAshape abstraction maps structures to a tree-like domain of shapes.

plassembler

Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates