Software Updates

BEDOPS

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

merlin

uses sparse trees to represent gene flow in pedigrees and is a fast pedigree analysis package.

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.

tidk

Identify and find telomeres, or telomeric repeats in a genome.

alevin-fry

is a tool for the efficient processing of single-cell data based on RAD files produced by alevin.

terminus

enables the discovery of data-driven, robust transcript groups from RNA-seq data.

Longshot

a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).

mudskipper

is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.

seqcomplexity

calculates Per-Read and Total Sequence Complexity from FastQ file.

vapor

is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis.

flexbar

preprocesses high-throughput sequencing data efficiently

10xbamtofastq

tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis.

LiftoffTools

is a toolkit to compare genes lifted between genome assemblies.

vembrane

allows to simultaneously filter variants based on any INFO field, CHROM, POS, REF, ALT, QUAL, and the annotation field ANN.

popscle

is a suite of population scale analysis tools for single-cell genomics data.

pLannotate

is web server for automatically annotating engineered plasmids.