Synteny and Rearrangement Identifier (SyRI) SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI identifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations, and duplications), local variations (SNPs, indels, CNVs etc) within syntenic and structural rearrangements, and un-aligned regions.
SyRI uses an unprecedented approach where it starts by identifying longest syntenic path (set of co-linear regions).
What is tldr-pages? The tldr-pages project is a collection of community-maintained help pages for command-line tools, that aims to be a simpler, more approachable complement to traditional man pages.
Maybe you are new to the command-line world? Or just a little rusty? Or perhaps you can’t always remember the arguments to lsof, or tar?
Location and version:
1 2 3 4 $ which tldr /local/cluster/bin/tldr $ tldr --version tldr 2.
funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at http://funannotate.readthedocs.io
To activate, check out a node with qrsh and run:
1 2 bash source /local/cluster/funannotate/activate.sh To use in SGE_Batch, write a shell script that includes the above source line, then the commands you would like to run.
Location and version:
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.
Location and version:
1 2 3 4 5 6 7 8 9 $ which FastTree /local/cluster/bin/FastTree $ which FastTreeMP /local/cluster/bin/FastTreeMP $ which FastTreeDbl /local/cluster/bin/FastTreeDbl $ FastTree -expert Detailed usage for FastTree 2.
wfmash - A DNA sequence read mapper based on mash distances and the wavefront alignment algorithm wfmash is a fork of MashMap that implements base-level alignment using WFA, via the wflign tiled wavefront global alignment algorithm. It completes MashMap with a high-performance alignment module capable of computing base-level alignments for very large sequences.
Location and version:
1 2 $ which wfmash /local/cluster/bin/wfmash help message:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 $wfmash-hwfmash[target][queries.
Pavian - interactive browser application for omics data Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome.
Location and version:
1 2 3 4 $ bash $ source /local/cluster/pavian/activate.sh $ Rscript -e "packageVersion('pavian')" [1] ‘1.2.0’ A wrapper script has been provided to facilitate the use of interactive pavian sessions.
