Tools   Select Another Resource Report Type

https://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en

Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories.

Proper citation: ProCon - PROteomics CONversion (RRID:SCR_016363) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://web.stanford.edu/group/pritchardlab/structure.html

Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms.

Proper citation: STRUCTURE (RRID:SCR_017637) Copy   

•   Source: SciCrunch Registry

https://github.com/isovic/racon

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

Proper citation: Racon (RRID:SCR_017642) Copy   

•   Source: SciCrunch Registry

https://github.com/Brazelton-Lab/seq-annot

Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.

Proper citation: seq-annot (RRID:SCR_018731) Copy   

•   Source: SciCrunch Registry

https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry

https://qupath.github.io/

Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.

Proper citation: QuPath (RRID:SCR_018257) Copy   

•   Source: SciCrunch Registry

https://chlorobox.mpimp-golm.mpg.de/geseq.html

Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.

Proper citation: GeSeq (RRID:SCR_017336) Copy   

•   Source: SciCrunch Registry

https://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry

https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny

Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.

Proper citation: halSynteny (RRID:SCR_018127) Copy   

•   Source: SciCrunch Registry

https://github.com/almorlio/CiLiQuant

Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.

Proper citation: CiLiQuant (RRID:SCR_019319) Copy   

•   Source: SciCrunch Registry

https://github.com/WorkflowConversion/CTDopts

Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities.

Proper citation: CTDopts (RRID:SCR_023997) Copy   

•   Source: SciCrunch Registry

https://github.com/jkbonfield/htscodecs/

Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data.

Proper citation: Htscodecs (RRID:SCR_024034) Copy   

•   Source: SciCrunch Registry

https://github.com/conda/conda-package-handling

Software to create and extract conda packages of various formats.

Proper citation: conda-package-handling (RRID:SCR_023991) Copy   

•   Source: SciCrunch Registry

http://www.cbcb.umd.edu/software/ELPH/index.shtml

Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).

Proper citation: ELPH (RRID:SCR_024011) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/alleleCount

Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings.

Proper citation: alleleCount (RRID:SCR_023961) Copy   

•   Source: SciCrunch Registry

https://github.com/mateidavid/fast5

Software C++ library for accessing Oxford Nanopore Technologies sequencing data.

Proper citation: Fast5 Library (RRID:SCR_024023) Copy   

•   Source: SciCrunch Registry

https://biom-format.org/

Software provides command line interface and Python API for working with Biological Observation Matrix files.

Proper citation: python-biom-format (RRID:SCR_024193) Copy   

•   Source: SciCrunch Registry