https://bioinformaticsonline.com/snippets?offset=50 https://bioinformaticsonline.com/snippets/view/43960/blast-short-sequences Wed, 21 Sep 2022 07:41:25 -0500 https://bioinformaticsonline.com/snippets/view/43960/blast-short-sequences (jitENV) [jnarayan@hn1 preetiDATA]$ blastn -task blastn -query list_flank_0.fa -subject ../monkeypoxDATA_07_06_22/JIT_gisaid_pox_2022_09_06_07.fasta -evalue 20000000 -word_size 5 -num_threads 4 -outfmt 6 -out blastn_0.txt -qcov_hsp_perc 100 -perc_identity 100 -max_target_seqs 10000]]> Jit https://bioinformaticsonline.com/snippets/view/43948/genome-scaffolding-and-gap-filling Wed, 24 Aug 2022 05:41:32 -0500 https://bioinformaticsonline.com/snippets/view/43948/genome-scaffolding-and-gap-filling scaffolding with ARCS v1.0.3 (−c3, −l,4, −a,0.9, −z500, −m50, −20 000, −e30000, −s90). https://github.com/bcgsc/arcs Next, automated gap filling was performed using Sealer v2.0.1 (−L150, -P10, −k75-115 [step = 10]) https://github.com/bcgsc/abyss/tree/sealer-release]]> Abhi https://bioinformaticsonline.com/snippets/view/43937/script-to-rapid-genome-clustering-based-on-pairwise-ani Tue, 09 Aug 2022 04:34:44 -0500 https://bioinformaticsonline.com/snippets/view/43937/script-to-rapid-genome-clustering-based-on-pairwise-ani First, create a blast+ database: makeblastdb -in <my_seqs.fna> -dbtype nucl -out <my_db> Next, use megablast from blast+ package to perform all-vs-all blastn of sequences: blastn -query <my_seqs.fna> -db <my_db> -outfmt '6 std qlen slen' -max_target_seqs 10000 -o <my_blast.tsv> -num_threads 32 Note: using the -perc_identity flag will speed up the search at the cost of sensitivity: blastn -query <my_seqs.fna> -db <my_db> -outfmt '6 std qlen slen' -max_target_seqs 10000 -perc_identity 90 -o <my_blast.tsv> -num_threads 32 Next, calculate pairwise ANI by combining local alignments between sequence pairs: anicalc.py -i <my_blast.tsv> -o <my_ani.tsv> Finally, perform UCLUST-like clustering using the MIUVIG recommended-parameters (95% ANI + 85% AF): aniclust.py --fna <my_seqs.fna> --ani <my_ani.tsv> --out <my_clusters.tsv> --min_ani 95 --min_tcov 85 --min_qcov 0]]> Neel https://bioinformaticsonline.com/snippets/view/43935/conda-command-to-install-checkv Mon, 08 Aug 2022 23:57:25 -0500 https://bioinformaticsonline.com/snippets/view/43935/conda-command-to-install-checkv (mENV) [jnarayan@hn1 Monkey_Pox]$ conda install -c conda-forge -c bioconda checkv Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/man/anaconda3/envs/jitENV added / updated specs: - checkv The following packages will be downloaded: package | build ---------------------------|----------------- boost-1.68.0 |py36h8619c78_1001 325 KB conda-forge boost-cpp-1.68.0 | h11c811c_1000 20.5 MB conda-forge ca-certificates-2022.6.15 | ha878542_0 149 KB conda-forge checkv-1.0.1 | pyhdfd78af_0 33 KB bioconda diamond-0.9.24 | ha888412_1 758 KB bioconda importlib-metadata-4.2.0 | py36h5fab9bb_0 30 KB conda-forge kcounter-0.1.1 | py36h91eb985_1 871 KB bioconda libzlib-1.2.12 | h166bdaf_2 63 KB conda-forge more-itertools-8.13.0 | pyhd8ed1ab_0 44 KB conda-forge openssl-1.1.1q | h166bdaf_0 2.1 MB conda-forge prodigal-gv-2.9.0 | h7132678_0 916 KB bioconda zipp-0.6.0 | py_0 7 KB conda-forge zlib-1.2.12 | h166bdaf_2 91 KB conda-forge ------------------------------------------------------------ Total: 25.9 MB The following NEW packages will be INSTALLED: biopython conda-forge/linux-64::biopython-1.79-py36h8f6f2f9_0 boost conda-forge/linux-64::boost-1.68.0-py36h8619c78_1001 boost-cpp conda-forge/linux-64::boost-cpp-1.68.0-h11c811c_1000 checkv bioconda/noarch::checkv-1.0.1-pyhdfd78af_0 diamond bioconda/linux-64::diamond-0.9.24-ha888412_1 importlib-metadata conda-forge/linux-64::importlib-metadata-4.2.0-py36h5fab9bb_0 kcounter bioconda/linux-64::kcounter-0.1.1-py36h91eb985_1 more-itertools conda-forge/noarch::more-itertools-8.13.0-pyhd8ed1ab_0 prodigal-gv bioconda/linux-64::prodigal-gv-2.9.0-h7132678_0 typing_extensions conda-forge/noarch::typing_extensions-3.10.0.2-pyha770c72_0 zipp conda-forge/noarch::zipp-0.6.0-py_0 The following packages will be UPDATED: libgcc-ng 11.2.0-h1d223b6_11 --> 12.1.0-h8d9b700_16 libzlib 1.2.11-h36c2ea0_1013 --> 1.2.12-h166bdaf_2 zlib 1.2.11-h36c2ea0_1013 --> 1.2.12-h166bdaf_2 The following packages will be SUPERSEDED by a higher-priority channel: ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.6.15-ha878542_0 openssl pkgs/main::openssl-1.1.1q-h7f8727e_0 --> conda-forge::openssl-1.1.1q-h166bdaf_0 Proceed ([y]/n)? y Downloading and Extracting Packages ca-certificates-2022 | 149 KB | ############################################################################################################################################################### | 100% openssl-1.1.1q | 2.1 MB | ############################################################################################################################################################### | 100% kcounter-0.1.1 | 871 KB | ############################################################################################################################################################### | 100% libzlib-1.2.12 | 63 KB | ############################################################################################################################################################### | 100% zlib-1.2.12 | 91 KB | ############################################################################################################################################################### | 100% more-itertools-8.13. | 44 KB | ############################################################################################################################################################### | 100% checkv-1.0.1 | 33 KB | ############################################################################################################################################################### | 100% zipp-0.6.0 | 7 KB | ############################################################################################################################################################### | 100% prodigal-gv-2.9.0 | 916 KB | ############################################################################################################################################################### | 100% importlib-metadata-4 | 30 KB | ############################################################################################################################################################### | 100% boost-cpp-1.68.0 | 20.5 MB | ############################################################################################################################################################### | 100% diamond-0.9.24 | 758 KB | ############################################################################################################################################################### | 100% boost-1.68.0 | 325 KB | ############################################################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: \ CheckV v1.0.1 an external database which needs to be downloaded and unarchived. The link for the database can be found in CheckV's instructions at https://bitbucket.org/berkeleylab/checkv/ done]]> Neel https://bioinformaticsonline.com/snippets/view/43915/install-read-simulator Sun, 10 Jul 2022 21:10:16 -0500 https://bioinformaticsonline.com/snippets/view/43915/install-read-simulator $ sudo apt install art-nextgen-simulation-tools [sudo] password for neelam: Reading package lists... Done Building dependency tree Reading state information... Done The following package was automatically installed and is no longer required: libfwupdplugin1 Use 'sudo apt autoremove' to remove it. The following additional packages will be installed: libgsl23 libgslcblas0 Suggested packages: art-nextgen-simulation-tools-profiles gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html The following NEW packages will be installed: art-nextgen-simulation-tools libgsl23 libgslcblas0 0 upgraded, 3 newly installed, 0 to remove and 1 not upgraded. Need to get 2,616 kB of archives. After this operation, 12.3 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu focal/universe amd64 libgslcblas0 amd64 2.5+dfsg-6build1 [84.6 kB] Get:2 http://in.archive.ubuntu.com/ubuntu focal/universe amd64 libgsl23 amd64 2.5+dfsg-6build1 [850 kB] Get:3 http://in.archive.ubuntu.com/ubuntu focal/universe amd64 art-nextgen-simulation-tools amd64 20160605+dfsg-4 [1,681 kB] Fetched 2,616 kB in 1s (4,578 kB/s) Selecting previously unselected package libgslcblas0:amd64. (Reading database ... 178334 files and directories currently installed.) Preparing to unpack .../libgslcblas0_2.5+dfsg-6build1_amd64.deb ... Unpacking libgslcblas0:amd64 (2.5+dfsg-6build1) ... Selecting previously unselected package libgsl23:amd64. Preparing to unpack .../libgsl23_2.5+dfsg-6build1_amd64.deb ... Unpacking libgsl23:amd64 (2.5+dfsg-6build1) ... Selecting previously unselected package art-nextgen-simulation-tools. Preparing to unpack .../art-nextgen-simulation-tools_20160605+dfsg-4_amd64.deb . .. Unpacking art-nextgen-simulation-tools (20160605+dfsg-4) ... Setting up libgslcblas0:amd64 (2.5+dfsg-6build1) ... Setting up libgsl23:amd64 (2.5+dfsg-6build1) ... Setting up art-nextgen-simulation-tools (20160605+dfsg-4) ... Processing triggers for libc-bin (2.31-0ubuntu9.9) ... Processing triggers for man-db (2.9.1-1) ...]]> Neel https://bioinformaticsonline.com/snippets/view/43891/bash-online-to-update-linux-os Tue, 14 Jun 2022 10:42:35 -0500 https://bioinformaticsonline.com/snippets/view/43891/bash-online-to-update-linux-os sudo bash -c 'for i in update {,full-,dist-}upgrade auto{remove,clean}; do apt-get $i -y; done']]> Surabhi Chaudhary https://bioinformaticsonline.com/snippets/view/43887/rename-the-screen-name-in-linux Mon, 30 May 2022 20:44:38 -0500 https://bioinformaticsonline.com/snippets/view/43887/rename-the-screen-name-in-linux screen -S 22798.pts-5.hn1 -X sessionname node33_COMPUTE]]> Shruti Paniwala https://bioinformaticsonline.com/snippets/view/43884/awk-command-to-keep-only-short-the-fasta-header Fri, 27 May 2022 03:36:41 -0500 https://bioinformaticsonline.com/snippets/view/43884/awk-command-to-keep-only-short-the-fasta-header awk '/^>/ {$0=$1} 1' file.fasta]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/43869/bash-command-to-remove-r Thu, 19 May 2022 05:53:20 -0500 https://bioinformaticsonline.com/snippets/view/43869/bash-command-to-remove-r VARNAME=$'a_bad_filename\r' VARNAME="${VARNAME%%[[:cntrl:]]}"]]> Neel https://bioinformaticsonline.com/snippets/view/43866/command-line-to-move-all-files-from-a-directory Wed, 18 May 2022 04:51:45 -0500 https://bioinformaticsonline.com/snippets/view/43866/command-line-to-move-all-files-from-a-directory find ~/Downloads/ -type f -print0 | xargs -0 mv -t ~/Videos]]> Neel