mcfonsecalab/htstools_plus repository overview

Dockerfile that includes a set of utilities for high throughput sequencing processing.

Image latest version: 0.6

• [Missing description of several tools]
• Subread⁠ - The Subread package: a tool kit for processing next-gen sequencing data. FeatureCounts, a counter mapped reads, is inside.
• MultiQC⁠ - Aggregate bioinformatics results across many samples into a single report. (version:1.9)
• samtools⁠ - A set of utilities that manipulate alignments in the SAM/BAM format. (version:1.10)
• bedtools2⁠ - A powerful toolset for genome arithmetic. (version:2.27.1)
• deeptools⁠ - deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data. (version:3.3.1)
• bamtools⁠ C++ toolit for working with BAM data. (version:2.5.0)
• faToTwoBit⁠ - Tool to convert DNA from fasta to .2bit format (Required for some GAT4 Spark tools).
• TrimGalore⁠ TrimGalore - A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. (version:0.6.5)
• FastQC⁠ - FastQC is a program designed to spot potential problems in high througput sequencing datasets. (version:0.11.9)