Differences
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| version [2020/08/31 10:49] – olivier | version [2024/03/29 09:46] – olivier | ||
|---|---|---|---|
| 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 69: | Line 76: | ||
| == Phylogeny == | == Phylogeny == | ||
| Beast | 1.10.4 | | | 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 83: | 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 109: | 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 123: | 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 144: | 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 152: | 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 164: | 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 189: | 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 199: | 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 204: | 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 | | | ||
version.txt · Last modified: 2024/05/03 13:33 by olivier