AUGUSTUS AUGUSTUS is a program to find genes and their structures in one or more genomes.
AUGUSTUS is a gene prediction program written or maintained by Mario Stanke, Oliver Keller, Stefanie König, Lizzy Gerischer, Katharina Hoff, Giovanna Migliorelli, Lars Gabriel, Anica Hoppe, Tonatiuh Peña Centeno, Henry Mehlan, Daniel Honsel and Steffen Herbold. It can be used as an ab initio program, which means it bases its prediction purely on the sequence.
w2rap-contigger An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.
Depends on the KAT analysis program.
To activate:
1 2 bash source /local/cluster/kat/activate.sh Location and version:
1 2 3 4 5 6 7 8 $ which w2rap-contigger /local/cluster/kat/bin/w2rap-contigger $ w2rap-contigger --version w2rap-contigger --version Welcome to w2rap-contigger w2rap-contigger version: 0.1 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 85 86 87 88 89 90 91 92 93 $ w2rap-contigger --help w2rap-contigger --help Welcome to w2rap-contigger USAGE: w2rap-contigger [-h] [--version] [-t <int>] [-m <int>] -r <file1.
interproscan What is InterProScan? InterPro is a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains.
Users who have novel nucleotide or protein sequences that they wish to functionally characterise can use the software package InterProScan to run the scanning algorithms from the InterPro database in an integrated way.
KAT - The K-mer Analysis Toolkit KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT:
hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting. gcp: K-mer GC Processor. Creates a matrix of the number of K-mers found given a GC count and a K-mer count.
Minimap2 Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-genome alignment between two closely related species with divergence below ~15%.
Snippy Rapid haploid variant calling and core genome alignment
Author Torsten Seemann
Synopsis Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder.
