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Automated generation of outputs
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@CallumWalley
CallumWalley committed Nov 24, 2024
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17 changes: 9 additions & 8 deletions outputs/dictionary.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -163,8 +163,6 @@ Bpipe's
Bpipe
Bracken's
Bracken
BreakDancer's
BreakDancer
BreakSeq2's
BreakSeq2
Broadwell
Expand Down Expand Up @@ -203,6 +201,8 @@ CPUs's
CPUs
CPU's
CPU
CRABS's
CRABS
CRAMINO's
CRAMINO
CRI
Expand Down Expand Up @@ -422,8 +422,6 @@ GLPK's
GLPK
GLib's
GLib
GLibmm's
GLibmm
GMAP-GSNAP's
GMAP-GSNAP
GMP's
Expand Down Expand Up @@ -819,6 +817,8 @@ Newton-X's
Newton-X
NextGenMap's
NextGenMap
NextPolish2's
NextPolish2
Nextflow's
Nextflow
Nim's
Expand Down Expand Up @@ -1349,6 +1349,7 @@ azul-zulu
backplane
bamUtil's
bamUtil
barcode
barrnap's
barrnap
basecaller
Expand Down Expand Up @@ -1695,8 +1696,8 @@ libpng's
libpng
libreadline's
libreadline
libsigc++'s
libsigc++
libsodium's
libsodium
libspatialite's
libspatialite
libtool's
Expand All @@ -1709,8 +1710,6 @@ libvdwxc's
libvdwxc
libxc's
libxc
libxml++'s
libxml++
libxml2's
libxml2
libxslt's
Expand Down Expand Up @@ -1741,6 +1740,8 @@ manta's
manta
mapDamage's
mapDamage
matlab-proxy's
matlab-proxy
meRanTK's
meRanTK
medaka's
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40 changes: 17 additions & 23 deletions outputs/glossary.md
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Expand Up @@ -63,7 +63,7 @@ AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0

## AOCL-BLIS:

Optimized version of FFTW for AMD EPYC family of processors..
Optimized version of BLIS for AMD EPYC family of processors..

## AOCL-FFTW:

Expand Down Expand Up @@ -360,10 +360,6 @@ A platform for running big bioinformatics jobs that consist of a series of proce
Hghly accurate statistical method that computes the abundance of
species in DNA sequences from a metagenomics sample.

## BreakDancer:

Genome-wide detection of structural variants from next generation paired-end sequencing reads.

## BreakSeq2:

Nucleotide-resolution analysis of structural variants
Expand Down Expand Up @@ -429,6 +425,10 @@ The CPMD code is a parallelized plane wave / pseudopotential implementation of D

Electronic circuitry that executes instructions of a computer program.

## CRABS:

Creating Reference databases for Amplicon-Based Sequencing.

## CRAMINO:

A tool for quick quality assessment of cram and bam files, intended for long read sequencing
Expand Down Expand Up @@ -853,10 +853,8 @@ Interface to Gd Graphics Library
GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for
data translation and processing.
NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB),
which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script)
after loading the GDAL module.
data translation and processing.
NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB), which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script) after loading the GDAL module.

## GEMMA:

Expand All @@ -879,10 +877,6 @@ GNU Linear Programming Kit is intended for solving large-scale linear programmin

GLib is one of the base libraries of the GTK+ project

## GLibmm:

C++ bindings for Glib

## GMAP-GSNAP:

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
Expand Down Expand Up @@ -1695,6 +1689,10 @@ NextGenMap is a flexible highly sensitive short read mapping tool that
handles much higher mismatch rates than comparable algorithms while still outperforming
them in terms of runtime.

## NextPolish2:

a fast and efficient genome polishing tool for long-read assembly

## Nextflow:

Nextflow is a reactive workflow framework and a programming DSL
Expand Down Expand Up @@ -2254,10 +2252,6 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg

Means of securely transferring files between over an SSH connection.

## SCons:

SCons is a software construction tool.

## SDL2:

Simple DirectMedia Layer, a cross-platform multimedia library
Expand Down Expand Up @@ -3522,9 +3516,9 @@ The GNU Readline library provides a set of functions for use by applications tha
The Readline library includes additional functions to maintain a list of previously-entered command lines,
to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

## libsigc++:
## libsodium:

The libsigc++ package implements a typesafe callback system for standard C++.
library for encryption, decryption, signatures, password hashing and more.

## libspatialite:

Expand Down Expand Up @@ -3556,10 +3550,6 @@ of density functional theory (DFT) codes.
Libxc is a library of exchange-correlation functionals for density-functional theory.
The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.

## libxml++:

libxml++ is a C++ wrapper for the libxml XML parser library.

## libxml2:

Libxml2 is the XML C parser and
Expand Down Expand Up @@ -3621,6 +3611,10 @@ Manta calls structural variants (SVs) and indels from mapped paired-end sequenci
tracks and quantifies DNA damage patterns among ancient
DNA sequencing reads generated by Next-Generation Sequencing platforms.

## matlab-proxy:

Python package which enables you to launch MATLAB and access it from a web browser.

## meRanTK:

High performance toolkit for complete analysis of methylated RNA data.
Expand Down
34 changes: 14 additions & 20 deletions outputs/snippets.md
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Expand Up @@ -33,8 +33,8 @@ annotate genetic variants detected from diverse genomes .
interpreting and visualizing multidimensional data.
*[AOCC's]: AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0
*[AOCC]: AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0
*[AOCL-BLIS's]: Optimized version of FFTW for AMD EPYC family of processors..
*[AOCL-BLIS]: Optimized version of FFTW for AMD EPYC family of processors..
*[AOCL-BLIS's]: Optimized version of BLIS for AMD EPYC family of processors..
*[AOCL-BLIS]: Optimized version of BLIS for AMD EPYC family of processors..
*[AOCL-FFTW's]: Optimized version of FFTW for AMD EPYC family of processors.
*[AOCL-FFTW]: Optimized version of FFTW for AMD EPYC family of processors.
*[AOCL-ScaLAPACK's]: Optimized version of ScaLAPACK for AMD EPYC family of processors.
Expand Down Expand Up @@ -265,8 +265,6 @@ sequencing reads to long reference sequences.
species in DNA sequences from a metagenomics sample.
*[Bracken]: Hghly accurate statistical method that computes the abundance of
species in DNA sequences from a metagenomics sample.
*[BreakDancer's]: Genome-wide detection of structural variants from next generation paired-end sequencing reads.
*[BreakDancer]: Genome-wide detection of structural variants from next generation paired-end sequencing reads.
*[BreakSeq2's]: Nucleotide-resolution analysis of structural variants
*[BreakSeq2]: Nucleotide-resolution analysis of structural variants
*[CCL's]: Clozure CL (often called CCL for short) is a free Common Lisp implementation
Expand Down Expand Up @@ -315,6 +313,8 @@ coverage data in multiple samples and linkage data from paired end reads.
*[CPUs]: Electronic circuitry that executes instructions of a computer program.
*[CPU's]: Electronic circuitry that executes instructions of a computer program.
*[CPU]: Electronic circuitry that executes instructions of a computer program.
*[CRABS's]: Creating Reference databases for Amplicon-Based Sequencing.
*[CRABS]: Creating Reference databases for Amplicon-Based Sequencing.
*[CRAMINO's]: A tool for quick quality assessment of cram and bam files, intended for long read sequencing
*[CRAMINO]: A tool for quick quality assessment of cram and bam files, intended for long read sequencing
*[CTPL's]: C++ Thread Pool Library
Expand Down Expand Up @@ -621,17 +621,13 @@ FreeSurfer contains a fully automatic structural imaging stream for processing c
*[GDAL's]: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for
data translation and processing.
NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB),
which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script)
after loading the GDAL module.
data translation and processing.
NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB), which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script) after loading the GDAL module.
*[GDAL]: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for
data translation and processing.
NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB),
which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script)
after loading the GDAL module.
data translation and processing.
NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB), which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script) after loading the GDAL module.
*[GEMMA's]: Genome-wide Efficient Mixed Model Association
*[GEMMA]: Genome-wide Efficient Mixed Model Association
*[GEOS's]: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
Expand All @@ -644,8 +640,6 @@ FreeSurfer contains a fully automatic structural imaging stream for processing c
*[GLPK]: GNU Linear Programming Kit is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems.
*[GLib's]: GLib is one of the base libraries of the GTK+ project
*[GLib]: GLib is one of the base libraries of the GTK+ project
*[GLibmm's]: C++ bindings for Glib
*[GLibmm]: C++ bindings for Glib
*[GMAP-GSNAP's]: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
GSNAP: Genomic Short-read Nucleotide Alignment Program
*[GMAP-GSNAP]: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
Expand Down Expand Up @@ -1297,6 +1291,8 @@ individuals fall into each of a set of user-defined hybrid categories.
*[NextGenMap]: NextGenMap is a flexible highly sensitive short read mapping tool that
handles much higher mismatch rates than comparable algorithms while still outperforming
them in terms of runtime.
*[NextPolish2's]: a fast and efficient genome polishing tool for long-read assembly
*[NextPolish2]: a fast and efficient genome polishing tool for long-read assembly
*[Nextflow's]: Nextflow is a reactive workflow framework and a programming DSL
that eases writing computational pipelines with complex data
*[Nextflow]: Nextflow is a reactive workflow framework and a programming DSL
Expand Down Expand Up @@ -1752,8 +1748,6 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg
*[SCOTCH]: Software package and libraries for sequential and parallel graph partitioning,
static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
*[SCP]: Means of securely transferring files between over an SSH connection.
*[SCons's]: SCons is a software construction tool.
*[SCons]: SCons is a software construction tool.
*[SDL2's]: Simple DirectMedia Layer, a cross-platform multimedia library
*[SDL2]: Simple DirectMedia Layer, a cross-platform multimedia library
*[SEPP's]: SATe-enabled Phylogenetic Placement. Phylogenetic placement of short reads into reference alignments and trees.
Expand Down Expand Up @@ -2699,8 +2693,8 @@ compression and decompression. libjpeg is a library that implements JPEG image e
allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available.
The Readline library includes additional functions to maintain a list of previously-entered command lines,
to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
*[libsigc++'s]: The libsigc++ package implements a typesafe callback system for standard C++.
*[libsigc++]: The libsigc++ package implements a typesafe callback system for standard C++.
*[libsodium's]: library for encryption, decryption, signatures, password hashing and more.
*[libsodium]: library for encryption, decryption, signatures, password hashing and more.
*[libspatialite's]: SpatiaLite is an open source library intended to extend the SQLite core to support
fully fledged Spatial SQL capabilities.
*[libspatialite]: SpatiaLite is an open source library intended to extend the SQLite core to support
Expand All @@ -2725,8 +2719,6 @@ of density functional theory (DFT) codes.
The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
*[libxc]: Libxc is a library of exchange-correlation functionals for density-functional theory.
The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
*[libxml++'s]: libxml++ is a C++ wrapper for the libxml XML parser library.
*[libxml++]: libxml++ is a C++ wrapper for the libxml XML parser library.
*[libxml2's]: Libxml2 is the XML C parser and
toolchain developed for the Gnome project
(but usable outside of the Gnome platform).
Expand Down Expand Up @@ -2771,6 +2763,8 @@ group MPI processes as an ordered set.
DNA sequencing reads generated by Next-Generation Sequencing platforms.
*[mapDamage]: tracks and quantifies DNA damage patterns among ancient
DNA sequencing reads generated by Next-Generation Sequencing platforms.
*[matlab-proxy's]: Python package which enables you to launch MATLAB and access it from a web browser.
*[matlab-proxy]: Python package which enables you to launch MATLAB and access it from a web browser.
*[meRanTK's]: High performance toolkit for complete analysis of methylated RNA data.
*[meRanTK]: High performance toolkit for complete analysis of methylated RNA data.
*[medaka's]: Medaka is a tool to create a consensus sequence from nanopore sequencing data.
Expand Down

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