btop++ Resource monitor that shows usage and stats for processor, memory, disks, network and processes. C++ version and continuation of bashtop and bpytop.
Features Easy to use, with a game inspired menu system. Full mouse support, all buttons with a highlighted key is clickable and mouse scroll works in process list and menu boxes. Fast and responsive UI with UP, DOWN keys process selection. Function for showing detailed stats for selected process.
rust-mdbg: Minimizer-space de Bruijn graphs (mdBG) for whole-genome assembly rust-mdbg is an ultra-fast minimizer-space de Bruijn graph (mdBG) implementation, geared towards the assembly of long and accurate reads such as PacBio HiFi.
Rationale rust-mdbg performs mdBG construction of a 52x human genome HiFi data in around 10 minutes on 8 threads, with 10GB of maximum RAM usage.
rust-mdbg is fast because it operates in minimizer-space, meaning that the reads, the assembly graph, and the final assembly, are all represented as ordered lists of minimizers, instead of strings of nucleotides.
gfatools gfa tools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED. More functionality may be added in future.
Location and version:
1 2 3 4 5 $ which gfatools /local/cluster/bin/gfatools $ gfatools version gfa.h: 0.5-r234 gfatools: 0.4-r214-dirty help message:
1 2 3 4 5 6 7 8 9 10 11 12 $ gfatools Usage: gfatools <command> <arguments> Commands: view read a GFA file stat statistics about a GFA file gfa2fa convert GFA to FASTA gfa2bed convert rGFA to BED (requiring rGFA) blacklist blacklist regions bubble print bubble-like regions (EXPERIMENTAL) asm miniasm-like graph transformation sql export rGFA to SQLite (requiring rGFA) version print version number software ref: https://github.
Kraken2 taxonomic sequence classification system Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.
The first version of Kraken used a large indexed and sorted list of k-mer/LCA pairs as its database.
piggy Piggy is a tool for analysing the intergenic component of bacterial genomes. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).
Location and version:
1 2 3 4 $ which piggy /local/cluster/bin/piggy $ piggy --version 1.5 help message:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 $ piggy --help Piggy - version 1.5 --in_dir|-i <STR> input folder [default - current folder] --out_dir|-o <STR> output folder [default - current folder/piggy_out] --roary_dir|-r <STR> folder where roary output is stored [required] --threads|-t <INT> threads [default - 1] --nuc_id|-n <INT> min percentage nucleotide identity [default - 90] --len_id|-l <INT> min percentage length identity [default - 90] --edges|-e keep IGRs at the edge of contigs [default - off] --size|-s <STR> size of IGRs to extract [i-j] [default 30-1000] --method|-m <STR> method for detecting switched IGRs [g - gene_pair, u - upstream] [default - g] --R_plots|-R make R plots (requires R, Rscript, ggplot2, reshape2) [default - off] --fast|-f fast mode (doesn't align IGRs or detect switched regions) [default - off] --help|-h help --version|-v version I suggest running roary in the same directory as the input gff files, then running piggy through with the --roary_dir .
Pandora Pandora is a tool for bacterial genome analysis using a pangenome reference graph (PanRG). It allows gene presence/absence detection and genotyping of SNPs, indels and longer variants in one or a number of samples. Pandora works with Illumina or Nanopore data. For more details, see our paper.
The PanRG is a collection of ‘floating’ local graphs (PRGs), each representing some orthologous region of interest (e.g. genes, mobile elements or intergenic regions).
