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version [2020/02/12 11:57] – olivierversion [2024/03/29 09:28] – 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 | 3.8.1551 | |+ Muscle | 5.1 | |
  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 | | 
 + 
 + == Metagenomics == 
 + Qiime | 2-2022.2 | | 
 + Mothur | 1.48.0 | | 
  == Trimmers / Reads cleaners ==  == Trimmers / Reads cleaners ==
  Bbmap | ? | |  Bbmap | ? | |
- Cutadapt | 1.11 | | + Cutadapt | 3.2 | | 
- 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 108:
  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 139:
  == 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 | 02/10/15 | |  Cap3 | 02/10/15 | |
  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 157:
  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 | 06/07/05 | |   Pcap | 06/07/05 | |
  PeakAnalyser | 1.4 | |  PeakAnalyser | 1.4 | |
Line 141: Line 184:
  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 193:
  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 206:
  big2bed,… | | |  big2bed,… | | |
  WebLogo/Seqlogo | 3.4 | 2.8.2 |  WebLogo/Seqlogo | 3.4 | 2.8.2 |
 + 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 221:
  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 233:
  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 245:
  == 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 253:
  
  == 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: 2024/03/29 09:46 by olivier

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