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.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

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.