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• Halla
  ...er, Emma Schwager,Jason Lloyd-Price, George Weingart, Yo Sup Moon, Xochitl C. Morgan, Levi Waldron, Eric A. Franzosa, Curtis Huttenhower. High-sensitivi
  3 KB (367 words) - 13:57, 25 March 2022
• Svtyper
  C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Mar
  3 KB (360 words) - 14:04, 3 October 2022
• MEGAHIT
  [https://www.ncbi.nlm.nih.gov/pubmed/25609793 Li, D., Liu, C-M., Luo, R., Sadakane, K., and Lam, T-W., (2015) MEGAHIT: An ultra-fast sin
  3 KB (367 words) - 18:31, 18 August 2022
• ViennaRNA
  The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and compar
  3 KB (396 words) - 19:08, 10 June 2022
• SHEsisPlus
  [1] Neigenfind J1, Gyetvai G, Basekow R, Diehl S, Achenbach U, Gebhardt C, Selbig J, Kersten B.Haplotype inference from unphased SNP data in heterozy
  3 KB (344 words) - 15:04, 19 August 2022
• FSL
  #M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:7 #M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data
  3 KB (365 words) - 16:47, 17 January 2023
• VS Code Remote Development
  # Use ''''Ctrl-C'''' key combination to stop the <code>tunnel</code> process. ...on requesting 4 cores, 15GB of RAM, an A100 GPU for 1 hour: <code>'''srun -c 4 --mem 15gb -p gpu --gres gpu:a100:1 -t 60 --pty bash -i'''</code>
  7 KB (1,100 words) - 17:42, 5 March 2024
• Csubst
  '''CSUBST''' is a tool for analyzing '''C'''ombinatorial '''SUBST'''itutions of codon sequences in phylogenetic trees
  3 KB (380 words) - 22:12, 26 July 2023
• MCarts
  Zhang, C. †, Lee, K.-Y., Swanson, M.S., Darnell, R.B. † 2013. Prediction of clus
  3 KB (399 words) - 14:53, 14 December 2022
• Open3d
  ...exposes a set of carefully selected data structures and algorithms in both C++ and Python. The backend is highly optimized and is set up for paralleliza
  3 KB (414 words) - 17:16, 7 July 2023
• TRNAscan-Se
  ...orithm from A. Pavesi's group). It runs on any UNIX system with Perl and a C compiler installed.
  3 KB (389 words) - 20:53, 12 August 2022
• Pygenometracks
  * Hi-C matrices (as triangle or squares)
  3 KB (375 words) - 20:54, 18 May 2023
• Caper
  ...a dependency of the [https://github.com/ENCODE-DCC/hic-pipeline ENCODE Hi-C uniform processing pipeline]. Caper wraps Cromwell to run pipelines on mult
  3 KB (425 words) - 14:43, 11 October 2023
• ITK-SNAP
  ...h, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User-guided 3D active contour segmentation of anatom
  3 KB (397 words) - 19:23, 12 August 2022
• Gblocks
  Gblocks is a computer program written in ANSI C language that eliminates
  3 KB (441 words) - 13:56, 13 June 2022
• Managing Python environments and Jupyter kernels
  mamba install cudatoolkit=11.3 pytorch=1.12.1=gpu_cuda* -c pytorch <code>mamba install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch</code>
  9 KB (1,496 words) - 16:52, 30 April 2024
• Julia
  ...written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal
  3 KB (412 words) - 20:49, 21 October 2022
• Artemis
  Carver T, Berriman M, Tivey A, Patel C, Böhme U et al.
  3 KB (378 words) - 14:53, 12 August 2022
• MMseqs2
  ...sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software
  3 KB (413 words) - 20:22, 2 October 2023
• VarSimLab
  Quit the server with CONTROL-C.
  3 KB (420 words) - 17:24, 22 August 2022
• Uproc
  ...ge-scale sequence analysis and is now available in terms of an open source C library. UProC is up to three orders of magnitude faster than profile-based
  3 KB (418 words) - 20:53, 12 August 2022
• Gem5
  gem5 is written primarily in C++ and python and most components are provided under a BSD style license. It
  3 KB (434 words) - 19:23, 10 June 2022
• SAMStat
  SAMStat is an efficient C program to quickly display statistics of large sequence files from next gen
  3 KB (429 words) - 20:34, 12 August 2022
• Chewiesnake
  Deneke C, Uelze L, Brendebach H, Tausch SH and Malorny B (2021)
  4 KB (457 words) - 15:02, 23 October 2023
• ART
  ...r the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART
  3 KB (440 words) - 21:10, 6 December 2019
• FAQ
  ...cProfile for python code, [[Nsight]] Compute for CUDA apps, or VTune for C/C++ + MPI code.
  7 KB (1,199 words) - 02:11, 17 April 2024
• MP-EST
  ...rees by maximizing a pseudo-likelihood function. The program is written in C. The parallel version of the program can run independent searches (chains)
  4 KB (489 words) - 12:01, 19 August 2022
• Reptile
  Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing
  3 KB (458 words) - 21:46, 21 August 2022
• Ea-utils
  :: Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It use
  4 KB (438 words) - 14:54, 15 August 2022
• Lazypipe
  ...taxonomic profiling of NGS libraries has been developed as a collection of C++, Perl and R scripts.
  4 KB (507 words) - 16:54, 14 December 2022
• PennCNV
  Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of
  4 KB (474 words) - 21:23, 6 December 2019
• Fast-Plast
  Marçais, G. and C. Kingsford. 2011. A fast, lock-free approach for efficient parallel countin
  4 KB (487 words) - 21:20, 6 December 2019
• Matlab
  ...mputing problems faster than traditional programming languages, such as C, C++, and Fortran. -rw-r--r-- 1 root root 2900 Apr 3 10:08 houdini_main.c
  9 KB (1,361 words) - 16:06, 28 November 2023
• SLURM Commands
  sinfo -o %P,%D,%c,%X,%m,%f
  4 KB (574 words) - 15:30, 25 April 2024
• GROMACS
  Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E.
  4 KB (556 words) - 19:16, 5 January 2023
• SnpEff
  *<pre>java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10</pre>
  4 KB (562 words) - 15:19, 5 January 2023
• Python
  ...load the environment module and run <code>pip list</code> or <code>python -c "help('modules')"</code> command before submitting a request for a new modu
  5 KB (670 words) - 19:42, 3 February 2023
• MetaBCC-LR
  -c 25000 \
  6 KB (774 words) - 14:28, 15 December 2022
• How To ResVault
  #* You can save data in the default C:\ drive, but it will be wiped out at the end of every session. Therefore, c
  6 KB (953 words) - 20:01, 18 July 2023
• Sate
  * Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, 2009. "Rapid and accurate large scale coestimation o * Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder. "SATé-II: Very Fast and Accurate Simultaneous Estimation of Mul
  7 KB (910 words) - 20:43, 21 December 2022
• Multi-Threaded & Message Passing Job Scripts
  *<code>-c, --cpus-per-task=<ncpus></code>
  9 KB (1,347 words) - 19:05, 21 July 2023
• Conda
  mamba install cudatoolkit=11.3 pytorch=1.12.1=gpu_cuda* -c pytorch
  16 KB (2,392 words) - 20:14, 16 April 2024
• User:Manoj
  FC="mpif90 -c" \ FC="mpif90 -c" \
  75 KB (8,369 words) - 08:47, 25 July 2013

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