Software Updates

Scallop

Scallop is an accurate reference-based transcript assembler.

MAFFT

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

ProPhyle

ProPhyle is an accurate, resource-frugal and deterministic phylogeny-based metagenomic classifier.

NanoPack

a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.

metagenome-atlas

ATLAS - Three commands to start analysing your metagenome data

MAFFT

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

fqgrep

is an approximate sequence pattern matcher for FASTQ/FASTA files.

bioinfokit

The bioinfokit toolkit aims to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments.

csvtk

a set of tools for manipulation of CSV/TSV files. It is convenient for rapid data investigation and integration into analysis pipelines.

spaceranger

Visium Spatial Software Suite for analyzing and visualizing spatial gene and protein expression data

R

a free software environment for statistical computing and graphics.

Unicycler

an assembly pipeline for bacterial genomes.

Cell Ranger

a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

UGENE

a free open-source bioinformatics software for macOS, and Linux.

SAIGE

an R package developed with Rcpp for genome-wide association tests in large-scale data sets and biobanks.

Julia

a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.

regenie

a C++ program for whole genome regression modelling of large genome-wide association studies.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Cactus

a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs.

GATK

(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.