Software Updates

DFAST

is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the INSDC.

vembrane

allows to simultaneously filter variants based on any INFO field, CHROM, POS, REF, ALT, QUAL, and the annotation field ANN.

DROP

(Detection of RNA Outlier Pipeline) pipeline to find aberrant gene expression events in RNA sequencing data.

Emacs

an extensible, customizable, free/libre text editor.

RSEM

(RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.

bioawk

an extension to Brian Kernighan's awk, with added support for several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q, and TAB-delimited formats with column names along with new built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk should behave exactly like the original BWK awk.

Horovod

Distributed training framework for TensorFlow, Keras, PyTorch, and Apache MXNet.

TensorFlow

an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, and the flexible numerical computation core is used across many other scientific domains.

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.

Foldseek

a program that enables fast and sensitive comparisons of large structure sets.

bamtools

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