NgsCcts
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This page documents apps installed by the CCTS BMI group in cheaha:/share/apps/ngs-ccts
Links to latest versions of each package are in /share/apps/ngs-ccts/latest.
See also PublicDatasetsNgs for genomes, indices and databases
Microbiome
R-packages
Alignment Visualization
Short Read Aligners
- [ tophat]
- tophat-2.0.6 (binary)
- bowtie
- bowtie-0.12.7 (linked from Galaxy)
- bowtie-0.12.8 (binary)
- bowtie2
- bowtie2-2.0.0-beta7 (download binary)
- bwa
- bwa-0.6.2 (download src) NgsCctsBuildBwa
- MOSAIK
- mosaik-1.1.0021 - installed in galaxy
- mosaik-2.1 exe_dist too old, must build from source (download src) NgsCctsBuildMosaik
Short Read (denovo) Assemblers
- velvet
- velvet_1.2.08 (download src)(NgsCctsBuildVelvet)
- MAXKMERLENGTH = 57
- LONGSEQUENCES
- velvet_1.2.08 (download src)(NgsCctsBuildVelvet)
SNP analysis
- SnpEff
- snpeff_3_1 (zip)
- scripted install of galaxy wrappers galaxy/tools/snpEff/_install_from.sh
- gene indexes for all available genomes downloaded and install
- 1112 genomes, 4.8G
- data in /scratch/share/public_datasets/ngs/databases/snpEff/3_1/data
- parallel download script /scratch/share/public_datasets/ngs/scripts/databases/snpEff/qsub_download_snpEff_genome
- snpeff_3_1 (zip)
Pairwise Sequence Alignment
- GeneWise (compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors)
- wise2.2.0 (donload binary) NgsCctsGeneWise
in process
- ABySS NOT DONE
- abyss_1.3.4 (download src)(NgsCctsBuildAbyss)
- maxk=100
- abyss_1.3.4 (download src)(NgsCctsBuildAbyss)
- VICUNA from Broad Institute (NgsCctsBuildVicuna) - Viral genome denovo assembler NOT DONE