Difference between revisions of "Bioinformatics Software"

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! Name !! Description
 
! Name !! Description
 
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| Bamtools || BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files
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| [Bamtools]https://github.com/pezmaster31/bamtools || BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files
 
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| Macs2 || Model Based Analysis for ChIP-Seq data
 
| Macs2 || Model Based Analysis for ChIP-Seq data
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| Mafft || Multiple alignment program for amino acid or nucleotide sequences
 
| Mafft || Multiple alignment program for amino acid or nucleotide sequences
 
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| Tobias || TOBIAS - Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
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| Tobias || Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
 
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| Weblogo || Web based application designed to make the generation of sequence logos as easy and painless as possible
 
| Weblogo || Web based application designed to make the generation of sequence logos as easy and painless as possible

Revision as of 14:38, 18 June 2020

Name Description
[Bamtools]https://github.com/pezmaster31/bamtools BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files
Macs2 Model Based Analysis for ChIP-Seq data
Mafft Multiple alignment program for amino acid or nucleotide sequences
Tobias Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
Weblogo Web based application designed to make the generation of sequence logos as easy and painless as possible

Software installed in Bioinformatics cluster

PEAKachu

Peak calling tool for CLIP-seq data

Github

To use run this command

module load peakachu

FastUniq

An ultrafast de novo tool for removal of duplicates in paired short DNA sequence reads in FASTQ format

SourceForge

cmpfastq

A simple Perl program that allows the user to compare QC filtered fastq files

Home page


STAR

Ultrafast universal RNA-seq aligner

Github

Installed version: 2.7.3a


Bedtools

Bedtools is a fast, flexible toolset for genome arithmetic.

Webpage

Installed version: 2.29.0

Usage:

module load bedtools

GATK

Genome Analysis Toolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.

The tools can be used individually or chained together into complete workflows.

Webpage

Installed version: 4.1.3.0

Usage:

module load gatk

SourceTracker2

SourceTracker is a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments.

Webpage

Usage:

module load conda-st2