Software Updates

Minimap2

is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments.

UPIMAPI

(UniProt Id Mapping through API) a command line interface for using UniProt's API, which allows access to UniProt's ID mapping programmatically.

RSeQC

(RNA-seq Quality Control Package) provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.

MultiQC

aggregates results from bioinformatics analyses across many samples into a single report.

SeqKit

a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing.

TaxonKit

a command-line toolkit for rapid manipulation of NCBI taxonomy data.

Nextstrain

real-time tracking of pathogen evolution.

TRF

(Tandem Repeats Finder) a program to locate and display tandem repeats in DNA sequences.

SeqKit

a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing.

GSAlign

an ultra-fast sequence alignment algorithm for intra-species genome comparison.

razers3

faster, fully sensitive read mapping.

PopDel

(Population-wide Deletion Calling) fast structural deletion calling on population-scale short read paired-end germline WGS data.

HyPhy

(Hypothesis Testing using Phylogenies) an open-source software package for comparative sequence analysis using stochastic evolutionary models.

gsort

a tool to sort genomic files according to a genomefile.

Comet

Comet MS/MS searches uninterpreted tandem mass spectra of peptides against sequence databases.

Sickle

a windowed adaptive trimming tool for FASTQ files using quality.

Alfred

an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner.

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

NGLess

(NGS Processing with Less Work) enables creation of a pipeline of work for all the first phase of NGS analysis until the point (inclusive) of annotation.

PyMOL Open Source

open source version of the widely used molecular visualization package developed by Warren DeLano.

NanoVar

a genomic structural variant (SV) caller that utilizes low-depth long-read sequencing such as Oxford Nanopore Technologies (ONT).

somalier

extracts informative sites, evaluates relatedness, and performs quality-control on BAM/CRAM/BCF/VCF/GVCF.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.

IQ-TREE

efficient and versatile phylogenomic software by maximum likelihood.

ENANO

a FASTQ lossless compression algorithm especially designed for nanopore sequencing FASTQ files.

elPrep

a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines.

nanoplexer

a standard tool to demultiplex Nanopore long read sequencing data.

segemehl

a software to map short sequencer reads to reference genomes.

SURVIVOR

a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

SViCT

a computational tool for detecting structural variations from cell free DNA (cfDNA) containing low dilutions of circulating tumor DNA (ctDNA).

sansa

Structural variant (SV) annotation.