hifiasm Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads. It can assemble a human genome in several hours and assemble a ~30Gb California redwood genome in a few days. Hifiasm emits partially phased assemblies of quality competitive with the best assemblers. Given parental short reads or Hi-C data, it produces arguably the best haplotype-resolved assemblies so far. Location and version: 1 2 3 4 $ which hifiasm /local/cluster/bin/hifiasm $ hifiasm --version 0.

PPanGGOLiN : Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species.

canu Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/ Sequel or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences Location and version: 1 2 3 4 $ which canu /local/cluster/canu/bin/canu $ canu --version canu 2.

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.

samtools Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants HTSlib A C library for reading/writing high-throughput sequencing data Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

ipa - Improved Phased Assembly Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with input reads and resulting in a polished assembly. IPA is fast, providing an easy to use local run mode or a distributed pipeline for a cluster. To activate: