savytskanatalia

yay![2] Updated STAR (v.2.7.5a)

conda-based multiqc installation (as for some reason multiqc/multiqc does not work for me)

Minimap2+bwa-mem2

minimap2 for all sorts of read mapping

Dockerfile for more or less painless bcl2fastq Illumina installation.

Metagenomic image-kit

quanTEfication2+BBMap mapper

Multiple MSAs? Phylogenetic trees? Consensus tree? All in one.

Yay!

Docker image instance for fastp tool used for preprocessing and QC of raw sequencing data

Docker image for V-pipe, 10.1101/2020.06.09.142919

Docker Image with TElocal v.1.0 installed. https://github.com/mhammell-laboratory/TElocal

Docker image for SQuIRE, Software for Quantifying Interspersed Repeat Expression.

Different alignment tools, that can be used in some mode for RNAseq mapping

All te quantifiers I wanted to have a look at in one place.

for splicing

Metagenomics toolset, including Kraken 2 (annotation) and Bracken (abundance of species estimation).

Kraken2.0.7-beta Metagenomics EDITED

cage_pipeline_2.0

R-base, Python3, TagDust 2.33, skewer (adaptor trimmer), STAR 2.6.0a (RNAseq-aligner)

Centrifuge is a novel microbial classification engine. https://ccb.jhu.edu/software/centrifuge/