...
Software | Description | Access |
---|---|---|
JupyterHub Server | Python Notebook Server | Available on all compute servers https://<server_name>.ccbb.utexas.edu |
R Studio Server | R Studio Web Interface |
Standard OS Software
(where in repo? frep -r pattern .| grep -v /spec/)
Software | Description |
---|---|
build-essential | gcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool |
emacs, vi, vim, ed | text editors |
postfix | mail programs |
perl | perl interpretor |
python 2 | python version 2 interpretor |
python 3 | python version 3 interpretor |
ruby | ruby programming language |
samba | Windows SMB/CIFS file and printer sharing protocol and applications |
screen, tmux | Text window managers (multiplexer) |
ssh | Secure Shell (remote access) |
sudo | Root access for POD delegates only |
tar | File archiving utility |
wget, curl | Remote file/url transfer utilities |
gzip, zip, unzip | File compression and archiving tools. |
scons | Software build tool |
swig | Software development tool |
sqlite3 | SQL Lite databases |
git | Version control utilities |
Standard BioLinux Packages
(how to check versions? dpkg -l bioperl) check R modules in common.yaml
Software | Version | Description | in cqb-biolinux? |
---|---|---|---|
2.0.2-3 | de novo, parallel, sequence assembler for short reads | y | |
bamtools | 2.4.1+dfsg-2 | toolkit for manipulating BAM (genome alignment) files | y |
bedtools | 2.26.0+dfsg-5 | suite of utilities for comparing genomic features | y |
bioperl | 1.7.2-2 | Perl tools for computational molecular biology | y |
bioperl-run | 1.7.1-3 | BioPerl wrappers: scripts | y |
blast2 | 1:2.6.0-1 | Basic Local Alignment Search Tool | y |
bowtie | 1.2.2+dfsg-2 | Ultrafast memory-efficient short read aligner | y |
bowtie2 | 2.3.4.1-1 | Ultrafast memory-efficient short read aligner | |
bwa | 0.7.17-1ubuntu0.1 | Burrows-Wheeler Aligner | |
cd-hit | 4.6.8-1 | a suite of programs designed to quickly group sequences | y |
clustalw | 2.1+lgpl-5 | No description | y |
clustalx | 2.1+lgpl-6 | No description | y |
cufflinks | 2.2.1+dfsg.1-2 | Transcript assembly, differential expression and regulation for RNA-Seq | |
ea-utils | 1.1.2+dfsg-4build1 | command-line tools for processing biological sequencing data | y |
emboss | 6.6.0+dfsg-6build1 | european molecular biology open software suite | |
emboss-lib | 6.6.0+dfsg-6build1 | EMBOSS Libraries | y |
fastdnaml | 1.2.2-12 | Tool for construction of phylogenetic trees of DNA sequences | y |
fastqc | 0.11.5+dfsg-6 | A quality control application for high throughput sequence data | |
fastx-toolkit | 0.0.14-5 | FASTQ/A short nucleotide reads pre-processing tools | y |
hmmer | 3.1b2+dfsg-5ubuntu1 | profile hidden Markov models for protein sequence analysis | |
jaligner | 1.0+dfsg-4 | Smith-Waterman algorithm with Gotoh’s improvement | y |
jellyfish | 2.2.8-3build1 | count k-mers in DNA sequences | y |
khmer | 2.1.2+dfsg-3 | k0.7.17-1ubuntu0.1-mer counting, filtering and graph traversal | y |
libbiojava-java | 1:1.7.1-7 | Java API to biological data and applications (default version) | y |
libbiojava-java-demos | 1:1.7.1-7 | Example programs for BioJava | y |
macs | 2.1.1.20160309-2 | Model-based Analysis of ChIP-Seq on short reads sequencers | y |
mafft | 7.310-1 | Multiple alignment program for amino acid or nucleotide sequences | y |
maq | 0.7.1-7 | maps short fixed-length polymorphic DNA sequence reads to reference sequences | y |
med-bio | 3.0.1ubuntu1 | Debian Med bioinformatics packages | y |
med-cloud | 3.0.1ubuntu1 | Debian Med bioinformatics applications usable in cloud computing | y |
microbiomeutil | 20101212+dfsg1-1build1 | Microbiome Analysis Utilities | y |
mothur | 1.39.5-2build1 | sequence analysis suite for research on microbiota | y |
mothur-mpi | 1.39.5-2build1 | mpi-enabled binary for mothur | y |
mrbayes-mpi | 3.2.6+dfsg-2 | Bayesian Inference of Phylogeny – mpi version | y |
mummer | 3.23+dfsg-3 | Efficient sequence alignment of full genomes | y |
muscle | 1:3.8.31+dfsg-3 | Multiple alignment program of protein sequences | y |
ncbi-blast+ | 2.6.0-1 | next generation suite of BLAST sequence search tools | |
ncbi-blast+-legacy | 2.6.0-1 | NCBI Blast legacy call script | |
ncbi-seg | 0.0.20000620-4 | tool to mask segments of low compositional complexity in amino acid sequences | y |
ncbi-tools-bin | 6.1.20170106-2 | NCBI libraries for biology applications (text-based utilities) | y |
ncbi-tools-x11 | 6.1.20170106-2 | NCBI libraries for biology applications (X-based utilities) | y |
paml | 4.9g+dfsg-3 | Phylogenetic Analysis by Maximum Likelihood (PAML) | y |
parafly | 0.0.2013.01.21-3build1 | parallel command processing using OpenMP | y |
phylip | 1:3.696+dfsg-5 | No description | y |
phyml | 3:3.3.20170530+dfsg-2 | Phylogenetic estimation using Maximum Likelihood | y |
picard-tools | 2.8.1+dfsg-3 | Command line tools to manipulate SAM and BAM files | y |
primer3 | 2.4.0-1ubuntu2 | Tool to design flanking oligo nucleotides for DNA amplification | y |
pymol | 1.8.4.0+dfsg-1build1 | Molecular Graphics System | y |
qiime | 3:3.3.20170530+dfsg-2 (1.8.0+dfsg-4ubuntu1)? | Quantitative Insights Into Microbial Ecology | y |
rasmol | 2.7.5.2-2 | Visualize biological macromolecules | y |
raxml | 8.2.11+dfsg-1 | Randomized Axelerated Maximum Likelihood of phylogenetic trees | y |
readseq | 1-12 | Conversion between sequence formats | y |
rsem | 1.2.31+dfsg-1 | RNA-Seq by Expectation-Maximization | y |
samtools | 1.7-1 | processing sequence alignments in SAM and BAM formats | |
sift | 4.0.3b-6 | predicts if a substitution in a protein has a phenotypic effect | y |
sortmerna | 2.1-2 | tool for filtering, mapping and OTU-picking NGS reads | y |
stacks | 2.0Beta8c+dfsg-1 | pipeline for building loci from short-read sequences | y |
sumatra | 1.0.31-1 | fast and exact comparison and clustering of sequences | y |
swarm | 2.2.2+dfsg-1 | robust and fast clustering method for amplicon-based studies | y |
t-coffee | 2.2.2+dfsg-1 (11.00.8cbe486-6) | Multiple Sequence Alignment | |
tophat | 2.1.1+dfsg1-1 | fast splice junction mapper for RNA-Seq reads | |
transdecoder | 5.0.1-1 | find coding regions within transcripts | y |
trinityrnaseq | 2.5.1+dfsg-2 | RNA-Seq De novo Assembly | y |
trnascan-se | 1.3.1-1 | search for tRNA genes in genomic sequences | y |
velvet | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads | y |
velvet-example | 1.2.10+dfsg1-3build1 | Example data for the Velvet sequence assembler | y |
velvet-long | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads, long version | y |
velvetoptimiser | 2.2.6-1 | Automatically optimise Velvet do novo assembly parameters | y |
vsearch | 2.7.1-1 | tool for processing metagenomic sequences | y |
zsh | 5.4.2-3ubuntu3.1 | shell with lots of features | y |
...
Software | Description | Version |
---|---|---|
R, Rscript | R command-line shell and script execution programs. | 3.4.4, 3.5.3, 3.6.1 |
Matlab | MathWorks Matlab Software. See How do I use MATLAB on the POD? |
Additional
...
Python Tools
(cqb-devel_tools/manifests/python.pp) find version with pip (pip3 freeze | grep xopen)
Software | Python2 Version | Python3 Version | Description | in devel_tools |
---|---|---|---|---|
all-dev | y | |||
blaze | 0.10.1 | 0.10.1 | An interface to query data on different storage systems | y |
cutadapt | 1.18 | 1.18 | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | y |
dendropy | phylogenetic computing | y | ||
freetype-dev (libfreetype6-dev) | This package contains all of the supplementary files you need to develop your own programs using the FreeType 2 library. | y | ||
leukgen-disambiguate | 1.0.1 | 1.0.1 | Disambiguate reads mapping to multiple genomes. This is a frozen release with some bug fixes of the original AstraZeneca-NGS/disambiguate v1.0. | y |
MACS2 | 2.1.2 | Model Based Analysis for ChIP-Seq data | y | |
maplot | 1.0.2 | 1.0.2 | Python package for creating interactive MA-plots | y |
matplotlib | 2.1.1 | 3.2.1 | python 2D plotting library | y |
networkx | 2.2 | 2.0 | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | y |
nimfa | 1.3.4 | 1.3.4 | Nonnegative matrix factorization | y |
numpy | 1.13.3 | 1.13.3 | scientific computing with Python | y |
pandas | 0.22.0 | 0.22.0 | Python Data Analysis Library | y |
patsy | 0.4.1+dev | 0.2.1 | Patsy is a Python library for describing statistical models (especially linear models, or models that have a linear component) and building design matrices. Patsy brings the convenience of R “formulas” to Python. | y |
pip | Python installation program (to install python modules) | y | ||
plotly | 4.0.0 | 4.0.0 | An open-source, interactive data visualization library for Python | y |
pysam | 0.8.4 | 0.8.4 | a python module for reading, manipulating and writing genomic data sets | y |
pyvttbl | 0.5.2.2 | 0.5.2.2 | Multidimensional pivot tables, data processing, statistical computation | y |
reportlab (->biopython?) | 3.4.0 (->1.70) | 3.5.12 (->1.73) | The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics. (→ Freely available tools for computational molecular biology) | y |
rpy2 | 2.8.6 | 2.9.2 | Python interface to R | y |
seaborn | 0.8.1 | 0.8.1 | statistical data visualization | y |
scipy | 0.19.1 | 0.19.1 | Collection of Python software for mathematics, science, and engineering. | y |
sklearn | Machine Learning in Python | y | ||
skimage | Image processing in Python | y | ||
statsmodels | 0.8.0 | 0.8.0 | Estimation of statistical models | y |
Additional R Tools
(cqbhiera/common.yaml dont appear to have versions)
Software | Description | in common.yaml | listed in library() |
---|---|---|---|
abind | GNU R package “Combine multi-dimensional arrays” | y | y |
ade4 | GNU R package “Analysis of Ecological Data : Exploratory | y | |
ape | GNU R package “Analyses of Phylogenetics and Evolution” | y | |
bitops | GNU R package implementing bitwise operations | y | |
blogdown | Create Blogs and Websites with R Markdown | y | y |
bookdown | Authoring Books and Technical Documents with R Markdown | y | y |
catools | GNU R package “Tools: moving window statistics, GIF, | y | y |
car | Companion to Applied Regression | y | y |
cargo | y | ||
cluster | GNU R package for cluster analysis by Rousseeuw et al | y | |
colourpicker | A Colour Picker Tool for Shiny and for Selecting Colours in Plots | y | y |
cowplot | Streamlined Plot Theme and Plot Annotations for 'ggplot2' | y | y |
curl | A Modern and Flexible Web Client for R | y | y |
data.table | GNU R package “Extension of data.frame” | y | |
dbi | GNU R package “R Database Interface” | ||
dbplyr | R Database Interface | y | y |
dendextend | Extending 'dendrogram' Functionality in R | y | |
dichromat | Color schemes for dichromats | y | |
digest | GNU R package “Create Cryptographic Hash Digests of R | y | |
emmeans | Estimated Marginal Means, aka Least-Squares Means | y | y |
evaluate | GNU R package “Parsing and Evaluation Tools that Provide | y | |
fivethirtyeight | Data and Code Behind the Stories and Interactives at 'FiveThirtyEight' | y | y |
forcats | Data and Code Behind the Stories and Interactives at 'FiveThirtyEight' | y | y |
foreach | Provides Foreach Looping Construct | y | y |
futile.logger | GNU R package “A Logging Utility for R” | y | |
futile.options | GNU R package “Futile options management” | y | |
gdata | GNU R package “Various R Programming Tools for Data | y | |
getopt | GNU R package “C-like getopt behavior.” | ||
gganimate | A Grammar of Animated Graphics | y | y |
GGally | Extension to 'ggplot2' | y | y |
ggExtra | Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements | y | y |
ggplot2 | GNU R package “An Implementation of the Grammar of | y | |
ggpubr | 'ggplot2' Based Publication Ready Plots | y | y |
ggrepel | Automatically Position Non-Overlapping Text Labels with 'ggplot2' | y | y |
ggsci | Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2' | y | y |
ggsignif | Significance Brackets for 'ggplot2' | y | y |
gifski | Highest Quality GIF Encoder | y | y |
glmnet | Lasso and Elastic-Net Regularized Generalized Linear Models | y | y |
gplots | GNU R package “Various R Programming Tools for Plotting | y | |
gridSVG | Export 'grid' Graphics as SVG | y | y |
gtable | GNU R package “Arrange grobs in tables.” | y | |
gtools | GNU R package “Various R Programming Tools” | y | |
haven | Import and Export 'SPSS', 'Stata' and 'SAS' Files | y | y |
igraph | Network Analysis and Visualization | y | y |
interactions | Comprehensive, User-Friendly Toolkit for Probing Interactions | y | y |
jpeg | Read and write JPEG images | y | y |
labeling | GNU R package “Axis Labeling” | y | |
lambda.r | GNU R package “Modeling Data with Functional Programming” | y | |
lattice | GNU R package “Lattice Graphics” | y | |
latticeExtra | Extra Graphical Utilities Based on Lattice | y | y |
leaps | GNU R package “regression subset selection” | y | y |
libssl-dev | prereq? | y | |
libcairo2-dev | perreq? | y | |
libxt-dev | prereq? | y | |
libgmp10 | prereq? | y | |
libgmp-dev | prereq? | y | |
libmpfr6 | prereq? | y | |
libmpfr-dev | prereq? | y | |
lme4 | GNU R package for linear mixed effects model fitting | y | y |
locfit | Local Regression, Likelihood and Density Estimation | y | y |
lubridate | Make Dealing with Dates a Little Easier | y | y |
matrix | GNU R package of classes for dense and sparse matrices | y | |
matrixstats | R package “Methods that apply to rows and columns of a matrix” | y | |
mirbase.db | miRBase: the microRNA database | y | |
mixdist | Finite Mixture Distribution Models | y | y |
modelr | Modelling Functions that Work with the Pipe | y | y |
multcomp | Simultaneous Inference in General Parametric Models | y | y |
munsell | GNU R package “Munsell colour system” | y | |
mvtnorm | Multivariate Normal and t Distributions | y | y |
network | Classes for Relational Data | y | y |
nlme | GNU R package for (non-)linear mixed effects models | y | |
nloptr | R Interface to NLopt | y | y |
ontologyIndex | Functions for Reading Ontologies into R | y | y |
optparse | GNU R package “Command line option parser.” | ||
permute | GNU R package “Functions for Generating Restricted | ||
pheatmap | Pretty Heatmaps | y | y |
pbkrtest | Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison | y | y |
plotly | Create Interactive Web Graphics via 'plotly.js' | y | y |
plotROC | Generate Useful ROC Curve Charts for Print and Interactive Use | y | y |
plotrix | GNU R package “Various plotting functions” | y | y |
plyr | GNU R package “Tools for Splitting, Applying and Combining | y | |
polynom | A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations | y | y |
proto | GNU R package “Prototype object-based programming” | y | y |
quantmod | Quantitative Financial Modelling Framework | y | y |
quantreg | Quantile Regression | y | y |
r.methodss3 | GNU R package “Utility function for defining S3 methods” | y | |
rcolorbrewer | GNU R package providing suitable color palettes | y | |
rcpp | GNU R package “Seamless R and C++ Integration” | y | |
rcurl | GNU R package “General Network (HTTP/FTP/…) Client | y | |
relimp | GNU R package “Relative Contribution of Effects in a | y | |
reshape2 | GNU R package “Flexibly Reshape Data: A Reboot of the | y | y |
reticulate | Interface to 'Python' | y | y |
rggobi | GNU R package for the GGobi data visualization system | y | |
rgl | GNU R package for three-dimensional visualisation using OpenGL | ||
rgtk2 | GNU R binding for Gtk2 | ||
rmpi | GNU R package interfacing MPI libraries for distributed computing | y | |
RMySQL | Database Interface and 'MySQL' Driver for R | y | y |
ROCR | Visualizing the Performance of Scoring Classifiers | y | y |
rserve | GNU R Rserve tcp/ip server and sample clients | y | |
rstatix | Pipe-Friendly Framework for Basic Statistical Tests | y | y |
rsqlite | GNU R package “SQLite Interface for R” | y | |
rvest | Easily Harvest (Scrape) Web Pages | y | y |
scales | GNU R package “Scale Functions for Visualization” | y | |
scatterplot3d | GNU R package “3D Scatter Plot” | y | y |
servr | A Simple HTTP Server to Serve Static Files or Dynamic Documents | y | y |
Seurat | Tools for Single Cell Genomics | y | y |
shape | Functions for Plotting Graphical Shapes, Colors | y | y |
shiny | Web Application Framework for R | y | y |
shinyjs | Easily Improve the User Experience of Your Shiny Apps in Seconds | y | y |
sna | Tools for Social Network Analysis | y | y |
sp | GNU R package “Classes and Methods for Spatial Data” | ||
sqldf | Manipulate R Data Frames Using SQL | y | y |
statnet.common | Common R Scripts and Utilities Used by the Statnet Project Software | y | y |
stringr | GNU R package “Simple, Consistent Wrappers for Common | y | |
tcltk2 | GNU R package “Tcl/Tk Additions” | y | y |
testthat | GNU R package “Testthat code. Tools to make testing fun | y | |
tibble | Simple Data Frames | y | y |
tidyr | Tidy Messy Data | y | y |
tidyverse | Easily Install and Load the 'Tidyverse' | y | y |
transformr | Polygon and Path Transformations | y | y |
vegan | GNU R package “Community Ecology Package” | ||
VennDiagram | Generate High-Resolution Venn and Euler Plots | y | y |
VGAM | Vector Generalized Linear and Additive Models | y | y |
vioplot | Violin Plot | y | y |
xfun | Miscellaneous Functions by 'Yihui Xie' | y | y |
xml | GNU R package “Tools for Parsing and Generating XML Within | y | y |
xtable | GNU R coerce data to LaTeX and HTML tables | y |
Additional R BioConductor Tools
(cqbhiera/common.yaml) how to differentiate BioConductor tools
Software | Description | in common.yaml | in library() |
---|---|---|---|
affy | Methods for Affymetrix Oligonucleotide Arrays | y | y |
affyio | GNU R package “Tools for parsing Affymetrix data files” | y | |
annotate | GNU R package “Annotation for microarrays” | y | |
annotationdbi | GNU R package “Annotation Database Interface” | y | |
arrayQualityMetrics | Quality metrics report for microarray data sets | y | y |
ballgown | Flexible, isoform-level differential expression analysis | y | y |
biobase | GNU R package “Biobase: Base functions for Bioconductor” | y | |
biocgenerics | GNU R package “S4 generic functions for Bioconductor” | y | |
biocinstaller | GNU R package “Install/Update Bioconductor and CRAN | ||
biocparallel | GNU R package “Bioconductor facilities for parallel | y | |
biomart | GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) | y | |
biostrings | GNU R package “String objects representing biological | y | |
BSgenome | Efficient genome searching | y | y |
BSgenome.Hsapiens.UCSC.hg19 | Full genome sequences for Homo sapiens (UCSC version hg19) | y | y |
ChIPseeker | annotating ChIP-seq data analysis | y | y |
cummeRbund | analyzing Cufflinks RNA-Seq output | y | y |
deseq | |||
DESeq2 | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution | y | y |
devtools | Collection of package development tools | y | y |
DEXSeq | finding differential exon usage using RNA-seq exon counts between samples | y | y |
genefilter | GNU R package “genefilter: methods for filtering genes | y | |
geneplotter | Graphics related functions for Bioconductor | y | |
genomeinfodb | GNU R package “Utilities for manipulating chromosome and | y | |
genomicalignments | GNU R package “Representation and manipulation of short | y | |
genomicranges | GNU R package “Representation and manipulation of genomic | y | |
ggplot2movies | Movies Data | y | |
GISPA | GISPA: Method for Gene Integrated Set Profile Analysis | y | y |
GOstats | tools for interacting with GO and microarray data | y | y |
GO.db | y | ||
hilbertvis | GNU R package to visualise long vector data | ||
httpuv | HTTP and WebSocket Server Library | y | y |
iranges | GNU R package “Infrastructure for manipulating intervals | ||
JunctionSeq | JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data | y | y |
limma | GNU R package “Linear Models for Microarray Data” | y | |
mirbase.db | miRBase: the microRNA database | y | y |
multtest | GNU R package “Resampling-based multiple hypothesis | ||
org.Hs.eg.db | Genome wide annotation for Human | y | y |
org.Sc.sgd.db | Genome wide annotation for Yeast | y | y |
org.Mm.eg.db | Genome wide annotation for Mouse | y | y |
org.Rn.eg.db | Genome wide annotation for Rat | y | y |
preprocesscore | GNU R package “A collection of pre-processing functions” | y | |
processx | Execute and Control System Processes | y | y |
pkgload | y | ||
qvalue | Bioconductor package “Q-value estimation for false discovery rate control” | y | |
rhdf5 | provides an interface between HDF5 and R | y | y |
readr | Read Rectangular Text Data | y | y |
ReportingTools | Tools for making reports in various formats | y | y |
RIPSeeker | identify protein-associated transcripts from RIP-seq experiments | y | y |
roxygen2 | In-Line Documentation for R | y | y |
rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), | y | |
s4vectors | GNU R package “S4 implementation of vectors and lists” | y | |
SISPA | SISPA: Method for Sample Integrated Set Profile Analysis | y | y |
sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto | y | y |
ShortRead | sampling, iteration, and input of FASTQ files | y | y |
topGO | Enrichment Analysis for Gene Ontology | y | y |
TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | Annotation package for TxDb object(s) | y | y |
TxDb.Hsapiens.UCSC.hg38.knownGene | Annotation package for TxDb object(s) | y | y |
tximport | Import and summarize transcript-level estimates for transcript- and gene-level analysis | y | y |
WGCNA | Weighted Correlation Network Analysis | y | y |
xvector | GNU R package “Representation and manpulation of external | y | |
yardstick | Tidy Characterizations of Model Performance | y | y |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ | y |
Additional Perl CPAN modules
(cqbprofile/manifest/perl.pp and cqb-maker)
Software | Description | in perl.pp or cqb-maker? |
---|---|---|
Bit::Vector | y | |
CGI | y | |
DBI | y | |
DBD::SQLite | y | |
File::Which | y | |
forks | y | |
forks::shared | y | |
Graph | y | |
IO::All | y | |
IO:Prompt | y | |
LWP | y | |
Math::Cephes | y | |
Module::Build | y | |
Net::HTTP | y | |
Perl::Unsafe::Signals | y | |
Statistics::Descriptive | y | |
Switch | y | |
Test::Class | y | |
Test::More | y | |
Test::Exception | y | |
Test::Harness | y | |
XML::Simple | y |
Next Generation Sequencing (NGS) Tools
(cqbprofile/manifest/next_gen_sequencing_client.pp)
Software | Description | Path | in next_gen_sequencing_client.pp |
---|---|---|---|
bamtools | SAM/BAM file manipulation | /stor/system/opt/gitdir/bamtools/bin/bamtools | y |
bcl2fastq | BCL file manipulation | /usr/bin/bcl2fastq | y |
deeptools | y | ||
enabrowsertools | y | ||
hisat | y | ||
fastq_screen | |||
guppy | y | ||
samtools | SAM/BAM file manipulation | /usr/bin/samtools /usr/bin/samtools_0.1.18 /usr/bin/samtools-1.3 | |
picard | SAM/BAM file manipulation | /stor/system/opt/picard-tools-1.141 /stor/system/opt/picard-tools-2.5.0 | y |
bedtools | BED/GFF file manipulation | /usr/bin/bedtools-2.17.0 /usr/bin/bedtools-2.25.0 | y |
samtools | y | ||
scalangs | y | ||
sra toolkit | SRA file manipulation | /stor/system/opt/sratoolkit.2.7.0-ubuntu64 | y |
stringtie | y | ||
bwa | Alignment | /usr/bin/bwa |
RNA Sequencing Tools
(cqbprofile/manifest/rna_sequencing_client.pp)
Software | Description | Path | in rna_sequencing_client.pp |
---|---|---|---|
augustus | y | ||
busco | y | ||
cellranger | y | ||
cufflinks | y | ||
express | Expression quantification | /usr/bin/express | y |
fastqc | y | ||
featurecounts | Counting | /usr/bin/featureCounts | y |
htseq | Counting | /stor/system/opt/HTSeq-0.6.1p1 | y |
kallisto | Expression quantification | /usr/bin/kallisto | y |
STAR | Alignment | /usr/bin/STAR /usr/bin/STARlong | y |
tophat | y | ||
MultiQC | Report Generation | /usr/bin/multiqc | y |
RNA-SeQC | QC of RNA-seq alignments. To run this Java program: java -jar /stor/system/opt/rnaseqc/RNA-SeQC_v1.1.8.jar <other options> | /stor/system/opt/rnaseqc | y |
salmon | y | ||
hisat | Spliced alignment for mapping RNA-seq reads | /stor/system/opt/hisat-0.1.6-beta | |
hisat2 | Align NGS reads (both DNA and RNA) against a reference genome | /stor/system/opt/hisat2-2.0.5/ |
Specialized NGS Tools
(specialized_sequencing_client.pp)
Software | Description | Path | in specialized_sequencing_client.pp |
---|---|---|---|
BWA | y | ||
bwa_mem2 | y | ||
MultiQC | Report Generation | /usr/bin/multiqc | |
eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen | y |
imageJ | y | ||
meme suite | motif analysis | /stor/system/opt/meme_4.11.2 | |
meme_chip | motif analysis suite for ChIP-seq | /stor/system/opt/software/meme-chip/4.11.2/ | y |
art | next generation sequencing read simulator | /usr/bin/art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD | y |
...
Molecular Structures Client
Software | Description | Path | in molecular_structures_client.pp |
---|---|---|---|
mgltools |
POD-specific software (look for these)
...