Sidebar
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Tools on IRCAN's server
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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 | 2.4.1 | 1.1.2 | BSseeker2 | 2.1.8 | | BSseeker3 | 3 beta | | Bwa | 0.7.17 | | Gmap | 2015-12-31 | | Clustal Omega | 1.2.1 | | Clustalw | 2.1 | | Diamon | 2.0.13 | | Dorado | 0.3.4 | | Exonerate | 2.2.0 | | FastANI | 1.33 | | FastTree | 2.1.10 | | HiSat | 2.0.4 | 0.1.6-beta | Hmmer | 3.1b2 | 2.3.2 | Mafft | 7.310 | | Manta | 1.5.0 | | Mauve | Feb13_2015 | | Minimap2 | 2.24 | | MUMmer | 3.23 | | Muscle | 5.1 | | parnSNP | 1.2 | | Pbalign | 0.2.0.141024 | | Pblat | 35 | | Plast | 2.2.0b | | Prank | .1704272 | | Rmblastn | 2.2.27 | | Scapper | ? | | Snap | 1.0beta.23 | | FeatureCounts | 1.5.1 | | T_coffee | 11.00.8cbe486 | | TrimAL | v1.4 | | Usearch | v11 - 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 | |
== Phylogeny == Beast | 1.10.4 | | Beast | 2.x | | Beagle | ? | | GrapeTree | ? | | IQ-tree | 1.6.12 | | Poppunk | ? | |
== Quality control == Falco | 1.2.2 | | Fastqc | 0.12.0 | | PicoQC | 2.5.2 | |
== Metagenomics == Krona | 2.8.1 | | Qiime | 2-2022.2 | | Mothur | 1.48.0 | |
== Trimmers / Reads cleaners == Bbmap | ? | | Cutadapt | 3.2 | | FastP | 0.23.4 | | Fastq_screen | 0.15.1 | | Filtlong | 0.2.1 | | Multiqc | 1.12 | | Nanopack | 1.1.0 | | ParDRe | 2.2.5 | | Porechop | 0.2.4 | | Porechop_ABI | 0.5.1 | | Trimmomatic | 0.36 | | TrimGalore! | 0.4.2 | | == Assemblers == ABYSS | 2.0.2 | | AlignGraph | ? | | Canu | 2.3 | | Falcon-integrate| Nov.2016 | | Flye | 2.9-b1780 | | Lordec | 0.6 | | MarginPolish | 1.2 | | MaSuRCA | 3.1.3 | | Medusa | 1.6 | | MiniASM | ? | | Perga | 0.5.03.02 | | Pilon | 1.24 | | Quast | 5.2.0 | | Quiver | 2.0.0 | | Ragout | 1.2 | | Raca | ? | | Racon | 1.4.3 | | Shasta | 0.9 | | SmartDenovo | ? | | SPAdes | 3.15.5 | | Trinity | 2.14.0 | | Trycycler | 0.5.3 | | Unicyler | 0.5.0 | | wtdbg2 | 2.5 | |
== Scaffolders == Opera-lg | 2.0.6 | | Sspace | 3.0 | | Gapfiller | 1.0 | |
== Sequences Analysis == AdmixTools | ? | | Amos | 3.1.0 | | Any2fasta | 0.4.2 | | BedTools | 2.25.0 | 2.2.4 | BamTools | 2.4.0 | | Bedops | 2.4.26 | | Bcl2fastq | 2.17.1.14 | | Cactus | ? | | Cap3 | 02/10/15 | | Cd-hit | 4.7 | | ChewBBACA | 2.8.4 | | 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 | | Exomiser | 13.1.0 | | Fastq-scan | 1.0.0 | | FastTree | 2.1.10 | | Fastx_toolkit | 0.0.14 | | Gatb | 1.1.0 | | GenomeTools | 1.5.7 | | Giggle | 0.6.3 | | GTK | 3.6 | | HiCexplorer | 3.7.2 | | Homer | 4.7 | | Igv | 2.3 | | InterProScan | 5.17-56.0 | | Iq-Tree (conda) | ? | | Jellyfish | 2.2.10 | | Kallisto | 0.42.5 | | LIRCIAL | 1.3.4 | | MELT | 2.1.4 | | Methpat | 2.1.10 | | ncbi-genomes-dow| 0.3.1 | | orthoANI | 0.5.0 | | Ppanggolin(conda)| ? | | Pcap | 06/07/05 | | PeakAnalyser | 1.4 | | PeakAnnotator | 1.4 | | PeakSplitter | 1.0 | | PicardTools | 1.140 | | Platypus | - | | Poppunk (conda) | 2.4.0 | | Promals | - | | Pyseer | 1.1.1 | | Roary | ? | | Reptyr | 0.5 | | RepEnrich.py | 0.1 | | SalmonTE | 0.3 | | SamBamba | 0.6.5 | | SamTools | 1.2 | | Seqkit | 2.1.0 | | 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 | xTea | 0.1 | | == Sequences Analysis (ChIP-seq) == Epic2 | 0.0.16 | | Macs | 2.1.1 | 1.4.2 | Macs3 | 3.0.0 (conda) | | 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 | 2.7.5c | | 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 | 0.9 | | dna2pep | 1.1 | | GeneMark | ? | | Infernal | 1.1.1 | | Minced | 0.2.0 | | Pingpongpro | 1.0 | | Prodigal | 2.6.3 | | Rnammer | 1.2 | | SignalP | 4.1c | |
== Motifs Finder == Mash | 2.3 | | Perf | 0.4.5 | | Kmer-ssr | 0.8 | | RepeatMasker | 4.0.5 | | Trf | 4.0.7 | |
== Annotations ==
Abricate | 1.0.1 | | CPC2 | 0.1 | | Dfast | 1.2.18 | | Mlst | 2.23.0 | | Prokka | 1.11 | | Tbl2asn | 24.9 | |
== Other == Aspera | 3.5.4 | | Irods | ? | |
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Databases on IRCAN's server
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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
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version.txt · Last modified: 2024/12/17 14:59 by olivier