Software Updates

PBSIM2

PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores

Winnowmap

Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.

Flye

fast and accurate de novo assembler for single molecule sequencing reads.

perbase

Per-base metrics on BAM/CRAM files.

LRez

Standalone tool and library for working with barcoded linked-reads.

fpa

Filter Pairwise Alignment filter long read mapping information to save disk space

Rustyread

Rustyread, a long-read simulator

Genion

Characterizing gene fusions using long transcriptomics reads

Assembled Genomes Compressor

Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans).

TGS-GapCloser

A gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.

GraphAligner

Sequence to graph aligner for long reads

Fiji

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

megadepth

Megadepth is an efficient tool for extracting coverage related information from RNA and DNA-seq BAM and BigWig files.

ImageMagick

a software suite to create, edit, compose, or convert bitmap images.

Hifiasm

Haplotype-resolved assembler for accurate Hifi reads

Scallop-LR

reference-based transcriptome assembler for long-reads RNA-seq data

CITE-seq-Count

count antibody TAGS from a CITE-seq and/or cell hashing experiment.

dsh-bio

Tools for BED, FASTA, FASTQ, GAF, GFA1/2, GFF3, PAF, SAM, and VCF files

krakenuniq

Metagenomics classifier with unique k-mer counting for more specific results

DIAMOND

a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.

MethylDackel

MethylDackel will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.

deepTools

a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

pbmm2

pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in mapped concordance, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.

minorseq

PacBio Minor Variant Calling and Phasing Tools

bam2fastx

bam2fastx provides conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.