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~~~
—————————————————————————
Tools on IRCAN's server
—————————————————————————

Tools are in /scratch/bin. All executable were added to the $PATH, means that you can launch them from any location


 Name		| Cur. version	| Other versions	
--------------------------------------------------------

== Alignment ==
Bismark		| 0.17		|			|	
Blastn, Blastp…	| 2.2.31	|			|
Blat		| 36		|			|
Blasr		| 3.0.1		|			|
Bowtie		| 2.2.8		| 1.1.2			|
BSseeker2	| 2.1.8		|			|
BSseeker3	| 3 beta	|			|
Bwa		| 0.7.12-r1039	|			|
Gmap		| 2015-12-31	|			|
Clustal Omega	| 1.2.1		|			|
Clustalw	| 2.1		|			|
Exonerate	| 2.2.0		|			|
HiSat		| 2.0.4		| 0.1.6-beta		|
Hmmer		| 3.1b2		| 2.3.2			|
Mafft		| 7.310		|			|
Manta		| 1.5.0		|			|
Minimap2	| 2.17		|			|
MUMmer		| 3.23		|			|
Muscle		| 3.8.1551	|			|
parnSNP		| 1.2		|			|
Pbalign		| 0.2.0.141024	|			|
Pblat		| 35		|			|
Plast		| 2.2.0b	|			|
Prank		| .1704272	|			|
Rmblastn	| 2.2.27	|			|
Snap		| 1.0beta.23	|			|
FeatureCounts	| 1.5.1		|			|
T_coffee	| 11.00.8cbe486	|			|
Usearch		| v8.1 - 32bits	|			|
Vsearch		| v1.1.11	|			|
== Languages / Libraries ==

Perl		| 5.20.1	|			|
 Bioperl	| 1.6.910	|			|
 VCFtools	| 0.1.15	|			|
Python		| 2.7.8		| 3.4.1			|
 BioPython	| 1.68		|			|
 HTSeq		| 0.6.1		|			|
 Cruzdb		| 0.5		|			|
R		| 3.3.0		|			|
 Ade4		| 1.7-4		|			|
 Bioconductor	| 3.4		|			|
 ShortRead	|		|			|
 DESeq		| 1.24.0	| 			|
 DESeq2		| 1.12.3	| 			|
 EdgeR	 	|		|			|
 GenomicRanges	|		|			|
 GenomicFeatures|		|			|
 seqinr		| 3.1-3		|			|
 seqTools	|		|			|
 Ballgown	|		|			|
SciLab		| 5.5.2		|			|

== Trimmers / Reads cleaners ==
Bbmap		| ?		|			|
Cutadapt	| 1.11		|			|
FastP		| 0.19.4	|			|
Fastq_screen	| 0.8.0		|			|
ParDRe		| 2.2.5		|			|
Trimmomatic	| 0.36		|			|
TrimGalore!	| 0.4.2		|			|

== Assemblers ==

ABYSS		| 2.0.2		|			|
AlignGraph	| ?		|			|	
Canu		| 2		|			|
Falcon-integrate| Nov.2016	|			|	
Lordec		| 0.6		|			|
MarginPolish	| 1.2		|			|
MaSuRCA		| 3.1.3		|			|
MiniASM		| ?		|			|
Perga		| 0.5.03.02	|			|
Pilon		| 1.16		|			|
Quast		| 5.0.2		|			|
Quiver		| 2.0.0		|			|
Ragout		| 1.2		|			|
Raca		| ?		|			|
Racon		| 1.4.3		|			|
Shasta		| 0.3.0		|			|
SmartDenovo	| ?		|			|
SPAdes		| 3.8.0		|			|
Trinity		| 2.8.4		|			|
== Scaffolders ==

Opera-lg	| 2.0.6		|			|
Sspace		| 3.0		|			|
Gapfiller	| 1.0		|			|
== Sequences Analysis ==

Amos		| 3.1.0		| 			|
BedTools	| 2.25.0	| 2.2.4			|
BamTools	| 2.4.0		| 			|
Bedops		| 2.4.26	| 			|
Bcl2fastq	| 2.17.1.14	| 			|
Cap3		| 02/10/15	|			|
Cd-hit		| 4.7		|			|
Circos		| 0.69-3	|			|
Control-FREEC	| 10.6		|			|
CramTools	| 3.0		|			|
Cufflinks	| 2.2.1		|			|
DeNovoGear	| 0.5.4		|			|
Deeptools	| 1.5.9		|			|
EpiTEome	| 1.0		|			|
FastQ Screen	| 0.8.0		|			|
FastQValidator	| ?		|			|
FastTree	| 2.1.10	|			|
Fastx_toolkit	| 0.0.14	|			|
Gatb		| 1.1.0		|			|
GenomeTools	| 1.5.7		|			|
GTK		| 3.6		|			|
Homer		| 4.7		|			|
Igv		| 2.3		|			|
InterProScan	| 5.17-56.0	|			|
Jellyfish	| 2.2.10	|			|
Kallisto	| 0.42.5	|			|
MELT		| 2.1.4		|			|
Methpat		| 2.1.10	|			|
ncbi-genomes-dow| ?		|			|
Pcap		| 06/07/05	|			|	
PeakAnalyser	| 1.4		|			|
PeakAnnotator	| 1.4		|			|
PeakSplitter	| 1.0		|			|
PicardTools	| 1.140		|			|
Platypus	| -		|			|
Promals		| -		|			|	
Pyseer		| 1.1.1		|			|
Roary		| ?		|			|
Reptyr		| 0.5		|			|
RepEnrich.py	| 0.1		|			|
SalmonTE	| 0.3		|			|
SamBamba	| 0.6.5		|			|
SamTools	| 1.2		|			|
SeqTk		| 1.0-r82	|			|
SQuiRE		| 0.9.9.92	|			|
Sra-tool	| 2.5.4-1	|			|
 ncbi-vdb	|		|			|
 ncbi_ngss	| 		|			|
SWEMBL		| 3.6		|			|
TEtools		| 		|			|
TopHat		| 2.1.0		|			|
Ucsc tools 	| xxx		|			|
 liftover,…	| 		|			|
 big2bed,…	| 		|			|
WebLogo/Seqlogo	| 3.4		| 2.8.2			|

== Sequences Analysis (ChIP-seq) ==	
Epic2		| 0.0.16	|			|
Macs		| 2.1.1		| 1.4.2			|
PePr		| 1.1.10	|			|
Thor / Odin	| 0.1		|			|
== Sequences Analysis (RNA-Seq) ==	
Hisat pipeline	| ?		|			|
TEtranscripts	| 2.0.3		|			|
Salmon		| 0.11.4	|			|
Sleuth (R)	| -		|			|
Star		| 2.5.2a	|			|
StringTie	| 1.2.4		|			|
Suppa		| -		|			|
UMI_tools    	|   	  	|  	  	  	|
Wasabi (R)    	|   	  	|  	  	  	|

== Network Analysis ==	
MCL (+MCL-edge)	| 14-137	|			|
== Predictions tools ===
Aragorn		| 1.2.36	| 			|
Augustus	| 3.2.1		| 			|
Barrnap		| 0.7		| 			|
Infernal	| 1.1.1		| 			|
Minced		| 0.2.0		| 			|
Pingpongpro	| 1.0		|			|
Prodigal	| 2.6.3		|			|
Rnammer		| 1.2		|			|
SignalP		| 4.1c		|			|
== Motifs Finder ==

RepeatMasker	| 4.0.5	 	|			|
Trf		| 4.0.7		|			|
== Annotations ==

Prokka		| 1.11	 	|			|
Tbl2asn		| 24.9		|			|
== Other ==
	
Aspera		| 3.5.4		|			|
Irods		| ?		|			|

—————————————————————————
Databases on IRCAN's server
—————————————————————————

Databases are in /scratch/db
- Formated files for Blast are in /scratch/db/*/blastDB/
- Raw fasta files are in /scratch/db/
*/fastaDB/


 Description		| Versions		
--------------------------------------------------------

Human			| GRCh37, GRCH38
Danio rerio		| GRCz10
COG			| 2014

~~~

version.txt · Last modified: 2020/02/12 11:57 by olivier