Installed This software should be available with no extra configuration. trim_galore-0.6.7 For all high throughput sequencing applications, we would recommend performing some quality control on the data, as it can often straight away point you towards the next steps that need to be taken (e.g. with FastQC). Thorough quality control and taking appropriate steps to remove problems is vital for the analysis of almost all sequencing applications. This is even more critical for the proper analysis of RRBS libraries since they are susceptible to a variety of errors or biases that one could probably get away with in other sequencing applications.

Installed This software should be available with no extra configuration. ncbi-datasets-20221007 Note: syntax will be changing significantly in the version 14 release. Stay tuned… Getting started Welcome to NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. You have the choice of getting the data through three interfaces: NCBI Datasets website Command-line tools API: accessible through our Python package, or in combination with other UNIX tools (such as wget and curl).

Installed This software should be available with no extra configuration. gitui-0.21.0 Features Fast and intuitive keyboard only control Context based help (no need to memorize tons of hot-keys) Inspect, commit, and amend changes (incl. hooks: pre-commit,commit-msg,post-commit) Stage, unstage, revert and reset files, hunks and lines Stashing (save, pop, apply, drop, and inspect) Push/Fetch to/from remote Branch List (create, rename, delete, checkout, remotes) Browse commit log, diff committed changes Scalable terminal UI layout Async git API for fluid control Submodule support Location and version 1 2 3 4 $ which gitui /local/cluster/bin/gitui $ gitui --version gitui 0.

Installed This database should be available with no extra configuration. blastDB-20221005 BLAST DBs (nr and nt) have been updated. You will be able to use these if your $BLASTDB is properly set, which should be done for you automatically. If you need to use nt or nr, you can use them by specifying blastn -db nt or blastp -db nr as necessary. Location and version: 1 2 3 /nfs1/CGRB/databases/NCBI/v5/blast_20221005 $ echo $BLASTDB /nfs1/CGRB/BlastDB/NCBI/v5/latest_blast_DB software ref: https://ftp.

Installed This software should be available with no extra configuration. GMAP and GSNAP For GMAP and GSNAP documentation, please see the README or run helpme gmap from the command-line. Location and version 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 $ which gmap /local/cluster/gmap/bin/gmap $ gmap --version GMAP version 2021-12-17 called with args: gmap.sse42 --version GMAP: Genomic Mapping and Alignment Program Part of GMAP package, version 2021-12-17 Build target: x86_64-unknown-linux-gnu Features: pthreads enabled, no alloca, zlib available, mmap available, littleendian, sigaction available, 64 bits available Popcnt: mm_popcnt builtin_popcount Builtin functions: builtin_clz builtin_ctz builtin_popcount SIMD functions compiled: SSE2 SSSE3 SSE4.

Conda See the ‘activating the conda environment’ section below to access this software. seqenv Assign environment ontology (EnvO) terms to short DNA sequences. All code written by Lucas Sinclair. Publication at: https://peerj.com/articles/2690/ Usage Once that is done, you can start processing FASTA files from the command line. For using the default parameters you can just type: $ seqenv sequences.fasta We will then assume that you have inputed 16S sequences.