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version [2020/02/12 11:57] – olivier | version [2024/03/29 09:46] (current) – olivier | ||
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Line 17: | Line 17: | ||
Blat | 36 | | | Blat | 36 | | | ||
Blasr | 3.0.1 | | | Blasr | 3.0.1 | | | ||
- | Bowtie | 2.2.8 | 1.1.2 | | + | Bowtie | 2.4.1 | 1.1.2 | |
BSseeker2 | 2.1.8 | | | BSseeker2 | 2.1.8 | | | ||
BSseeker3 | 3 beta | | | BSseeker3 | 3 beta | | | ||
- | Bwa | 0.7.12-r1039 | | | + | Bwa | 0.7.17 | | |
Gmap | 2015-12-31 | | | Gmap | 2015-12-31 | | | ||
Clustal Omega | 1.2.1 | | | Clustal Omega | 1.2.1 | | | ||
Clustalw | 2.1 | | | Clustalw | 2.1 | | | ||
+ | Diamon | 2.0.13 | | | ||
+ | Dorado | 0.3.4 | | | ||
Exonerate | 2.2.0 | | | Exonerate | 2.2.0 | | | ||
+ | FastANI | 1.33 | | | ||
+ | FastTree | 2.1.10 | | | ||
HiSat | 2.0.4 | 0.1.6-beta | | HiSat | 2.0.4 | 0.1.6-beta | | ||
Hmmer | 3.1b2 | 2.3.2 | | Hmmer | 3.1b2 | 2.3.2 | | ||
Mafft | 7.310 | | | Mafft | 7.310 | | | ||
Manta | 1.5.0 | | | Manta | 1.5.0 | | | ||
- | Minimap2 | 2.17 | | | + | Mauve | Feb13_2015 | | |
+ | Minimap2 | 2.24 | | | ||
MUMmer | 3.23 | | | MUMmer | 3.23 | | | ||
- | Muscle | | + | Muscle | |
parnSNP | 1.2 | | | parnSNP | 1.2 | | | ||
Pbalign | 0.2.0.141024 | | | Pbalign | 0.2.0.141024 | | | ||
Line 38: | Line 43: | ||
Prank | .1704272 | | | Prank | .1704272 | | | ||
Rmblastn | 2.2.27 | | | Rmblastn | 2.2.27 | | | ||
+ | Scapper | ? | | | ||
Snap | 1.0beta.23 | | | Snap | 1.0beta.23 | | | ||
FeatureCounts | 1.5.1 | | | FeatureCounts | 1.5.1 | | | ||
T_coffee | 11.00.8cbe486 | | | T_coffee | 11.00.8cbe486 | | | ||
+ | TrimAL | v1.4 | | | ||
Usearch | v8.1 - 32bits | | | Usearch | v8.1 - 32bits | | | ||
Vsearch | v1.1.11 | | | Vsearch | v1.1.11 | | | ||
Line 66: | Line 73: | ||
Ballgown | | | | Ballgown | | | | ||
SciLab | 5.5.2 | | | 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 == | ||
+ | Qiime | 2-2022.2 | | | ||
+ | Mothur | 1.48.0 | | | ||
== Trimmers / Reads cleaners == | == Trimmers / Reads cleaners == | ||
Bbmap | ? | | | Bbmap | ? | | | ||
- | Cutadapt | | + | Cutadapt | |
- | FastP | 0.19.4 | | | + | FastP | 0.23.4 | | |
- | Fastq_screen | 0.8.0 | | | + | Fastq_screen | 0.15.1 | | |
+ | Filtlong | 0.2.1 | | | ||
+ | Multiqc | 1.12 | | | ||
+ | Nanopack | 1.1.0 | | | ||
ParDRe | 2.2.5 | | | ParDRe | 2.2.5 | | | ||
+ | Porechop | 0.2.4 | | | ||
Trimmomatic | 0.36 | | | Trimmomatic | 0.36 | | | ||
TrimGalore! | 0.4.2 | | | TrimGalore! | 0.4.2 | | | ||
Line 80: | Line 109: | ||
ABYSS | 2.0.2 | | | ABYSS | 2.0.2 | | | ||
AlignGraph | ? | | | AlignGraph | ? | | | ||
- | Canu | 2 | | | + | Canu | 2.3 | | |
- | Falcon-integrate| Nov.2016 | | | + | Falcon-integrate| Nov.2016 | | |
+ | Flye | 2.9-b1780 | | | ||
Lordec | 0.6 | | | Lordec | 0.6 | | | ||
MarginPolish | 1.2 | | | MarginPolish | 1.2 | | | ||
MaSuRCA | 3.1.3 | | | MaSuRCA | 3.1.3 | | | ||
+ | Medusa | 1.6 | | | ||
MiniASM | ? | | | MiniASM | ? | | | ||
Perga | 0.5.03.02 | | | Perga | 0.5.03.02 | | | ||
- | Pilon | 1.16 | | | + | Pilon | 1.24 | | |
- | Quast | 5.0.2 | | | + | Quast | 5.2.0 | | |
Quiver | 2.0.0 | | | Quiver | 2.0.0 | | | ||
Ragout | 1.2 | | | Ragout | 1.2 | | | ||
Raca | ? | | | Raca | ? | | | ||
Racon | 1.4.3 | | | Racon | 1.4.3 | | | ||
- | Shasta | 0.3.0 | | | + | Shasta | 0.9 | | |
SmartDenovo | ? | | | SmartDenovo | ? | | | ||
- | SPAdes | 3.8.0 | | | + | SPAdes | 3.15.5 | | |
- | Trinity | 2.8.4 | | | + | Trinity | 2.14.0 | | |
+ | Trycycler | 0.5.3 | | | ||
+ | Unicyler | 0.5.0 | | | ||
+ | wtdbg2 | 2.5 | | | ||
== Scaffolders == | == Scaffolders == | ||
Line 106: | Line 140: | ||
== Sequences Analysis == | == Sequences Analysis == | ||
+ | AdmixTools | ? | | | ||
Amos | 3.1.0 | | | Amos | 3.1.0 | | | ||
+ | Any2fasta | 0.4.2 | | | ||
BedTools | 2.25.0 | 2.2.4 | | BedTools | 2.25.0 | 2.2.4 | | ||
BamTools | 2.4.0 | | | BamTools | 2.4.0 | | | ||
Bedops | 2.4.26 | | | Bedops | 2.4.26 | | | ||
Bcl2fastq | 2.17.1.14 | | | Bcl2fastq | 2.17.1.14 | | | ||
+ | Cactus | ? | | | ||
Cap3 | 02/ | Cap3 | 02/ | ||
Cd-hit | 4.7 | | | Cd-hit | 4.7 | | | ||
+ | ChewBBACA | 2.8.4 | | | ||
Circos | 0.69-3 | | | Circos | 0.69-3 | | | ||
Control-FREEC | 10.6 | | | Control-FREEC | 10.6 | | | ||
Line 120: | Line 158: | ||
Deeptools | 1.5.9 | | | Deeptools | 1.5.9 | | | ||
EpiTEome | 1.0 | | | EpiTEome | 1.0 | | | ||
- | FastQ Screen | 0.8.0 | | | + | Exomiser | 13.1.0 | | |
- | FastQValidator | ? | | | + | Fastq-scan | 1.0.0 | | |
FastTree | 2.1.10 | | | FastTree | 2.1.10 | | | ||
Fastx_toolkit | 0.0.14 | | | Fastx_toolkit | 0.0.14 | | | ||
Gatb | 1.1.0 | | | Gatb | 1.1.0 | | | ||
GenomeTools | 1.5.7 | | | GenomeTools | 1.5.7 | | | ||
+ | Giggle | 0.6.3 | | | ||
GTK | 3.6 | | | GTK | 3.6 | | | ||
+ | HiCexplorer | 3.7.2 | | | ||
Homer | 4.7 | | | Homer | 4.7 | | | ||
Igv | 2.3 | | | Igv | 2.3 | | | ||
InterProScan | 5.17-56.0 | | | InterProScan | 5.17-56.0 | | | ||
+ | Iq-Tree (conda) | ? | | | ||
Jellyfish | 2.2.10 | | | Jellyfish | 2.2.10 | | | ||
Kallisto | 0.42.5 | | | Kallisto | 0.42.5 | | | ||
+ | LIRCIAL | 1.3.4 | | | ||
MELT | 2.1.4 | | | MELT | 2.1.4 | | | ||
Methpat | 2.1.10 | | | Methpat | 2.1.10 | | | ||
- | ncbi-genomes-dow| ? | | | + | ncbi-genomes-dow| 0.3.1 | | |
+ | orthoANI | 0.5.0 | | | ||
+ | Ppanggolin(conda)| ? | | | ||
Pcap | 06/ | Pcap | 06/ | ||
PeakAnalyser | 1.4 | | | PeakAnalyser | 1.4 | | | ||
Line 141: | Line 185: | ||
PicardTools | 1.140 | | | PicardTools | 1.140 | | | ||
Platypus | - | | | Platypus | - | | | ||
+ | Poppunk (conda) | 2.4.0 | | | ||
Promals | - | | | Promals | - | | | ||
Pyseer | 1.1.1 | | | Pyseer | 1.1.1 | | | ||
Line 149: | Line 194: | ||
SamBamba | 0.6.5 | | | SamBamba | 0.6.5 | | | ||
SamTools | 1.2 | | | SamTools | 1.2 | | | ||
+ | Seqkit | 2.1.0 | | | ||
SeqTk | 1.0-r82 | | | SeqTk | 1.0-r82 | | | ||
SQuiRE | 0.9.9.92 | | | SQuiRE | 0.9.9.92 | | | ||
Line 161: | Line 207: | ||
big2bed, | big2bed, | ||
WebLogo/ | WebLogo/ | ||
+ | xTea | 0.1 | | | ||
== Sequences Analysis (ChIP-seq) == | == Sequences Analysis (ChIP-seq) == | ||
Epic2 | 0.0.16 | | | Epic2 | 0.0.16 | | | ||
- | Macs | 2.1.1 | 1.4.2 | | + | Macs | 2.1.1 | 1.4.2 | |
+ | Macs3 | 3.0.0 (conda) | | | ||
PePr | 1.1.10 | | | PePr | 1.1.10 | | | ||
Thor / Odin | 0.1 | | | Thor / Odin | 0.1 | | | ||
Line 174: | Line 222: | ||
Salmon | 0.11.4 | | | Salmon | 0.11.4 | | | ||
Sleuth (R) | - | | | Sleuth (R) | - | | | ||
- | Star | 2.5.2a | | | + | Star | 2.7.5c | | |
StringTie | 1.2.4 | | | StringTie | 1.2.4 | | | ||
Suppa | - | | | Suppa | - | | | ||
Line 186: | Line 234: | ||
Aragorn | 1.2.36 | | | Aragorn | 1.2.36 | | | ||
Augustus | 3.2.1 | | | Augustus | 3.2.1 | | | ||
- | Barrnap | 0.7 | | | + | Barrnap | 0.9 | | |
+ | dna2pep | 1.1 | | | ||
+ | GeneMark | ? | | | ||
Infernal | 1.1.1 | | | Infernal | 1.1.1 | | | ||
Minced | 0.2.0 | | | Minced | 0.2.0 | | | ||
Line 196: | Line 246: | ||
== Motifs Finder == | == Motifs Finder == | ||
+ | Mash | 2.3 | | | ||
+ | Perf | 0.4.5 | | | ||
+ | Kmer-ssr | 0.8 | | | ||
RepeatMasker | 4.0.5 | | | RepeatMasker | 4.0.5 | | | ||
Trf | 4.0.7 | | | Trf | 4.0.7 | | | ||
Line 201: | Line 254: | ||
== Annotations == | == Annotations == | ||
- | + | ||
+ | Abricate | 1.0.1 | | | ||
+ | CPC2 | 0.1 | ||
+ | Dfast | 1.2.18 | | | ||
+ | Mlst | 2.23.0 | | | ||
Prokka | 1.11 | | | Prokka | 1.11 | | | ||
Tbl2asn | 24.9 | | | Tbl2asn | 24.9 | | |