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list-of-software [2021/09/20 07:50] – aorthlist-of-software [2022/02/22 13:24] – aorth
Line 24: Line 24:
 |[[artemis-software|artemis]]|16.0.0|''module load act/16.0.0''| | |[[artemis-software|artemis]]|16.0.0|''module load act/16.0.0''| |
 |[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| | |[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| |
-|[[awscli-software|awscli]]|1.17.9|''module load awscli/1.17.9''| |+|[[awscli-software|awscli]]|2.4.0|''module load awscli/2''| |
 |[[bam-readcount-software|bam-readcount]]|0.8.0|''module load bam-readcount/0.8.0''| | |[[bam-readcount-software|bam-readcount]]|0.8.0|''module load bam-readcount/0.8.0''| |
 |[[bamtools-software|bamtools]]|2.5.1|''module load bamtools/2.5.1''| | |[[bamtools-software|bamtools]]|2.5.1|''module load bamtools/2.5.1''| |
Line 31: Line 31:
 |[[bbmap-software|bbmap]]|38.67|''module load bbmap/38.67''| | |[[bbmap-software|bbmap]]|38.67|''module load bbmap/38.67''| |
 |[[bcftools-software|bcftools]]|1.13|''module load bcftools/1.13''| | |[[bcftools-software|bcftools]]|1.13|''module load bcftools/1.13''| |
 +|bcl2fastq|2.20.0.422|''bcl2fastq''| |
 |[[beagle-software|beagle]]|3.1.2|''module load beagle/3.1.2''| | |[[beagle-software|beagle]]|3.1.2|''module load beagle/3.1.2''| |
 |[[beast-software|beast]]|1.10.4|''module load beast/1.10.4''| | |[[beast-software|beast]]|1.10.4|''module load beast/1.10.4''| |
Line 40: Line 41:
 |[[bitseq-software|bitseq]]|0.7.5|''module load bitseq/0.7.5''| | |[[bitseq-software|bitseq]]|0.7.5|''module load bitseq/0.7.5''| |
 |[[blasr-software|blasr]]|smrtanalysis-4.0.0|''module load blasr/smrtanalysis-4.0.0''| | |[[blasr-software|blasr]]|smrtanalysis-4.0.0|''module load blasr/smrtanalysis-4.0.0''| |
-|[[blast-software|blast]]|2.10.0+|''module load blast/2.10.0+''| |+|[[blast-software|blast]]|2.12.0+|''module load blast/2.12.0+''| |
 |[[blobtools-software|blobtools]]|0.9.19.3|''module load blobtools/0.9.19.3''| | |[[blobtools-software|blobtools]]|0.9.19.3|''module load blobtools/0.9.19.3''| |
 |blat|06-Aug-2013|''module load blat/06-Aug-2013''| | |blat|06-Aug-2013|''module load blat/06-Aug-2013''| |
Line 46: Line 47:
 |[[bowtie2-software|bowtie2 ]]|2.3.4.1|''module load bowtie2/2.3.4.1''| | |[[bowtie2-software|bowtie2 ]]|2.3.4.1|''module load bowtie2/2.3.4.1''| |
 |[[brig-software|brig]]|0.95|''module load brig/0.95''| | |[[brig-software|brig]]|0.95|''module load brig/0.95''| |
-|[[busco-software|BUSCO ]]|4.0.6|''module load BUSCO/4.0.6''| |+|[[busco-software|BUSCO ]]|5.2.2|''module load BUSCO/5.2.2''| |
 |[[bwa-software|bwa]]|0.7.17|''module load bwa/0.7.17''| | |[[bwa-software|bwa]]|0.7.17|''module load bwa/0.7.17''| |
 |[[cafe-software|cafe]]|4.1|''module load cafe/4.1''| | |[[cafe-software|cafe]]|4.1|''module load cafe/4.1''| |
Line 69: Line 70:
 |[[corset-software|corset]]|1.06|''module load corset/1.06''| | |[[corset-software|corset]]|1.06|''module load corset/1.06''| |
 |cufflinks|2.2.1|''module load cufflinks/2.2.1''| | |cufflinks|2.2.1|''module load cufflinks/2.2.1''| |
-|[[cutadapt-software|cutadapt]]|1.18|''module load cutadapt/1.18''| |+|[[cutadapt-software|cutadapt]]|3.5|''module load cutadapt/3.5''| |
 |[[dextractor-software|dextractor]]|git-a7f50c52|''module load dextractor/git-a7f50c52''| | |[[dextractor-software|dextractor]]|git-a7f50c52|''module load dextractor/git-a7f50c52''| |
 |dendroscope|2.7.4|''module load dendroscope/2.7.4''| | |dendroscope|2.7.4|''module load dendroscope/2.7.4''| |
Line 86: Line 87:
 |[[fastp-software|fastp]]|0.22.0|''module load fastp/0.22.0''| | |[[fastp-software|fastp]]|0.22.0|''module load fastp/0.22.0''| |
 |[[fastPHASE-software|fastPHASE]]|1.4.8|''module load fastPHASE/1.4.8''| | |[[fastPHASE-software|fastPHASE]]|1.4.8|''module load fastPHASE/1.4.8''| |
-|[[fastqc-software|fastqc]]|0.11.7|''module load fastqc/0.11.7''| |+|[[fastqc-software|fastqc]]|0.11.9|''module load fastqc/0.11.9''| |
 |[[faststructure-software|fastSTRUCTURE]]|1.0|''module load fastSTRUCTURE/1.0''| | |[[faststructure-software|fastSTRUCTURE]]|1.0|''module load fastSTRUCTURE/1.0''| |
 |[[fasttree-software|fasttree]]|2.1.11|''module load fasttree/2.1.11''| | |[[fasttree-software|fasttree]]|2.1.11|''module load fasttree/2.1.11''| |
Line 96: Line 97:
 |[[flexbar-software|flexbar]]|2.7.0|''module load flexbar/2.7.8''| | |[[flexbar-software|flexbar]]|2.7.0|''module load flexbar/2.7.8''| |
 |[[flux-capacitor-software|flux-capacitor]]|1.6.1|''module load flux-capacitor/1.6.1''| | |[[flux-capacitor-software|flux-capacitor]]|1.6.1|''module load flux-capacitor/1.6.1''| |
-|[[flye-software|flye]]|2.8.1|''module load flye/2.8.1''| |+|[[flye-software|flye]]|2.9|''module load flye/2.9''| |
 |frappe|1.1|''module load frappe/1.1''| | |frappe|1.1|''module load frappe/1.1''| |
 |[[fraggenescan-software|FragGeneScan ]]|1.30|''module load fraggenescan/1.30''| | |[[fraggenescan-software|FragGeneScan ]]|1.30|''module load fraggenescan/1.30''| |
Line 123: Line 124:
 |[[hapflk-software|hapflk]]|1.4|''module load hapflk/1.4''| | |[[hapflk-software|hapflk]]|1.4|''module load hapflk/1.4''| |
 |hapmix|2.0|''module load hapmix/2.0''| | |hapmix|2.0|''module load hapmix/2.0''| |
 +|[[hawk-software|hawk]]|git-a177811d|''module load hawk/git-a177811d''| |
 |[[hclust2-software|hclust2]]|1.0.0|''module load hclust2/1.0.0''| | |[[hclust2-software|hclust2]]|1.0.0|''module load hclust2/1.0.0''| |
 |[[hdf5-software|hdf5]]|1.8.19|''module load hdf5/1.8.19''| | |[[hdf5-software|hdf5]]|1.8.19|''module load hdf5/1.8.19''| |
Line 149: Line 151:
 |[[juicebox-software|juicebox]]|1.11.08|''module load juicebox/1.11.08''| | |[[juicebox-software|juicebox]]|1.11.08|''module load juicebox/1.11.08''| |
 |[[juicer-software|juicer]]|1.6|''module load juicer/1.6''| | |[[juicer-software|juicer]]|1.6|''module load juicer/1.6''| |
-|[[kaiju-software|kaiju]]|1.4.4|''module load kaiju/1.4.4''| |+|[[kaiju-software|kaiju]]|1.8.2|''module load kaiju/1.8.2''| |
 |[[kallisto-software|kallisto]]|0.43.0|''module load kallisto/0.43.0''| | |[[kallisto-software|kallisto]]|0.43.0|''module load kallisto/0.43.0''| |
 |[[karect-software|karect]]|1.0|''module load karect/1.0''| | |[[karect-software|karect]]|1.0|''module load karect/1.0''| |
Line 164: Line 166:
 |[[lighter-software|lighter]]|1.1.2|''module load lighter/1.1.2''| | |[[lighter-software|lighter]]|1.1.2|''module load lighter/1.1.2''| |
 |[[lordec-software|lordec]]|0.9|''module load lordec/0.9''| | |[[lordec-software|lordec]]|0.9|''module load lordec/0.9''| |
 +|[[ltr_retriever-software|ltr_retriever]]|2.9.0|''module load ltr_retriever/2.9.0''| |
 |lucy|1.19p|''module load lucy/1.19p''| | |lucy|1.19p|''module load lucy/1.19p''| |
 |[[mafft-software|mafft]]|7.475|''module load mafft/7.475''| | |[[mafft-software|mafft]]|7.475|''module load mafft/7.475''| |
Line 179: Line 182:
 |[[mecat-software|MECAT]]|git-d04bfa84|''module load MECAT/git-d04bfa84''| | |[[mecat-software|MECAT]]|git-d04bfa84|''module load MECAT/git-d04bfa84''| |
 |[[medaka-software|medaka]]|1.4.3|''module load medaka/1.4.3''| | |[[medaka-software|medaka]]|1.4.3|''module load medaka/1.4.3''| |
-|[[megahit-software|megahit]]|1.1.4|''module load megahit/1.1.4''| |+|[[megahit-software|megahit]]|1.2.9|''module load megahit/1.2.9''| |
 |megan|4.70.4|''module load megan/4.70.4''| | |megan|4.70.4|''module load megan/4.70.4''| |
 |[[megax-software|megax]]|10.0.5|''module load megax/10.0.5''| | |[[megax-software|megax]]|10.0.5|''module load megax/10.0.5''| |
 |[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| | |[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| |
 +|[[metaeuk-software|metaeuk]]|git-9818d1a5|''module load metaeuk/git-9818d1a5''| |
 |[[metaphlan-software|metaphlan]]|3.0.13|''module load metaphlan/3.0.13''| | |[[metaphlan-software|metaphlan]]|3.0.13|''module load metaphlan/3.0.13''| |
 |[[metis-software|metis]]|5.1.0|''module load metis/5.1.0''| | |[[metis-software|metis]]|5.1.0|''module load metis/5.1.0''| |
Line 242: Line 246:
 |[[plink-software|plink]]|2.00-alpha|''module load plink/2.00-alpha''| | |[[plink-software|plink]]|2.00-alpha|''module load plink/2.00-alpha''| |
 |[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| | |[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| |
 +|[[poplddecay-software|poplddecay]]|3.41|''module load poplddecay/3.41''| |
 |[[porechop-software|porechop]]|0.2.4|''module load porechop/0.2.4''| | |[[porechop-software|porechop]]|0.2.4|''module load porechop/0.2.4''| |
 |[[pplacer-software|pplacer]]|1.1.alpha19|''module load pplacer/1.1.alpha19''| | |[[pplacer-software|pplacer]]|1.1.alpha19|''module load pplacer/1.1.alpha19''| |
Line 255: Line 260:
 |qdd|3_beta|''module load qdd/3_beta''| | |qdd|3_beta|''module load qdd/3_beta''| |
 |[[qiime-software|qiime]]|1.9.1|''module load qiime/1.9.1''| | |[[qiime-software|qiime]]|1.9.1|''module load qiime/1.9.1''| |
-|[[qiime2-software|qiime2]]|2020.8|''module load qiime2/2020.8''| |+|[[qiime2-software|qiime2]]|2021.8|''module load qiime2/2021.8''| |
 |[[quast-software|quast]]|5.0.2|''module load quast/5.0.2''| | |[[quast-software|quast]]|5.0.2|''module load quast/5.0.2''| |
 |[[quickmerge-software|quickmerge]]|0.3|''module load quickmerge/0.3''| | |[[quickmerge-software|quickmerge]]|0.3|''module load quickmerge/0.3''| |
Line 268: Line 273:
 |[[rdp-classifier-software|RDP Classifier]]|2.11|''module load rdp-classifier/2.11''| | |[[rdp-classifier-software|RDP Classifier]]|2.11|''module load rdp-classifier/2.11''| |
 |[[recon-software|recon]]|1.08|''module load recon/1.08''| | |[[recon-software|recon]]|1.08|''module load recon/1.08''| |
-|[[repeatmasker-software|repeatmasker]]|4.1.1|''module load repeatmasker/4.1.1''| |+|[[repeatmasker-software|repeatmasker]]|4.1.2-p1|''module load repeatmasker/4.1.2-p1''| |
 |[[repeatmodeler-software|repeatmodeler]]|2.0.1|''module load repeatmodeler/2.0.1''| | |[[repeatmodeler-software|repeatmodeler]]|2.0.1|''module load repeatmodeler/2.0.1''| |
 |[[repseqio-software|repseqio]]|1.3.3|''module load repseqio/1.3.3''| | |[[repseqio-software|repseqio]]|1.3.3|''module load repseqio/1.3.3''| |
Line 280: Line 285:
 |[[salmon-software|salmon]]|1.3.0|''module load salmon/1.3.0''| | |[[salmon-software|salmon]]|1.3.0|''module load salmon/1.3.0''| |
 |[[salsa-software|salsa]]|git-974589f3|''module load salsa/git-974589f3''| | |[[salsa-software|salsa]]|git-974589f3|''module load salsa/git-974589f3''| |
 +|[[satsuma2-software|satsuma2]]|git-37c5f386|''module load satsuma2/git-37c5f386''| |
 |[[scipio-software|scipio]]|1.4.1|''module load scipio/1.4.1''| | |[[scipio-software|scipio]]|1.4.1|''module load scipio/1.4.1''| |
 |[[scythe-software|scythe]]|0.994-beta|''module load scythe/0.994-beta''| | |[[scythe-software|scythe]]|0.994-beta|''module load scythe/0.994-beta''| |
-|[[sepp-software|sepp]]|4.3.8|''module load sepp/4.3.8''| |+|[[sepp-software|sepp]]|4.5.1|''module load sepp/4.5.1''| |
 |[[seroba-software|seroba]]|1.0.0|''module load seroba/1.0.0''| | |[[seroba-software|seroba]]|1.0.0|''module load seroba/1.0.0''| |
 |seq_crumbs|0.1.8|''module load seq_crumbs/0.1.8''| | |seq_crumbs|0.1.8|''module load seq_crumbs/0.1.8''| |
Line 296: Line 302:
 |[[smalt-software|smalt]]|0.7.6|''module load smalt/0.7.6''| | |[[smalt-software|smalt]]|0.7.6|''module load smalt/0.7.6''| |
 |[[smartdenovo-software|smartdenovo]]|git-5cc1356b|''module load smartdenovo/git-5cc1356b''| | |[[smartdenovo-software|smartdenovo]]|git-5cc1356b|''module load smartdenovo/git-5cc1356b''| |
-|[[snakemake-software|snakemake]]|5.7.0|''module load snakemake/5.7.0''| |+|[[snakemake-software|snakemake]]|6.15.5|''module load snakemake/6.15''| |
 |[[sniffles-software|sniffles]]|1.0.12b|''module load sniffles/1.0.12b''| | |[[sniffles-software|sniffles]]|1.0.12b|''module load sniffles/1.0.12b''| |
 |snowhite|1.1.4|''module load snowhite/1.1.4''| | |snowhite|1.1.4|''module load snowhite/1.1.4''| |
Line 308: Line 314:
 |[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|''module load SOAPdenovo-Trans/1.03''| | |[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|''module load SOAPdenovo-Trans/1.03''| |
 |[[solexaqa-software|SolexaQA++]]|3.1.3|''module load SolexaQA++/3.1.3''| | |[[solexaqa-software|SolexaQA++]]|3.1.3|''module load SolexaQA++/3.1.3''| |
-|[[spades-software|spades]]|3.13.0|''module load spades/3.13.0''| |+|[[spades-software|spades]]|3.15 (3.15.4)|''module load spades/3.15''| |
 |[[sourmash-software|sourmash]]|1.0|''module load sourmash/1.0''| | |[[sourmash-software|sourmash]]|1.0|''module load sourmash/1.0''| |
 |[[speedseq-software|speedseq]]|0.1.2|''module load speedseq/0.1.2''| | |[[speedseq-software|speedseq]]|0.1.2|''module load speedseq/0.1.2''| |
Line 326: Line 332:
 |tabix|git-76b4bbdf|''module load tabix/git-76b4bbdf''| | |tabix|git-76b4bbdf|''module load tabix/git-76b4bbdf''| |
 |[[tablet-software|tablet]]|1.17.08.17|''module load tablet/1.17.08.17''| | |[[tablet-software|tablet]]|1.17.08.17|''module load tablet/1.17.08.17''| |
-|[[tassel-software|tassel]]|4.0|''module load tassel/4.0''| |+|[[tassel-software|tassel]]|5.2.77|''module load tassel/5.2.77''| |
 |[[tmiseq-software|tmiseq]]|2016-01-31|''module load tmiseq/2016-01-31''| | |[[tmiseq-software|tmiseq]]|2016-01-31|''module load tmiseq/2016-01-31''| |
 |[[tophat-software|tophat]]|2.1.0|''module load tophat2/2.1.0''| | |[[tophat-software|tophat]]|2.1.0|''module load tophat2/2.1.0''| |
Line 333: Line 339:
 |[[transrate-software|Transrate]]|1.0.3|''module load transrate/1.0.3''|  | |[[transrate-software|Transrate]]|1.0.3|''module load transrate/1.0.3''|  |
 |[[trf-software|trf]]|4.0.9|''module load trf/4.0.9''| | |[[trf-software|trf]]|4.0.9|''module load trf/4.0.9''| |
 +|[[trimgalore-software|trimgalore]]|0.6.7|''module load trimgalore/0.6.7''| |
 |[[trimmomatic-software|trimmomatic]]|0.39|''module load trimmomatic/0.39''| | |[[trimmomatic-software|trimmomatic]]|0.39|''module load trimmomatic/0.39''| |
 |[[trinity-software|trinity]]|v2.11.0|''module load trinity/v2.11.0''| | |[[trinity-software|trinity]]|v2.11.0|''module load trinity/v2.11.0''| |
list-of-software.txt · Last modified: 2024/06/19 11:50 by aorth