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on page 1 showing 10 out of 10 results

Cite this (BinPacker, RRID:SCR_017038)

URL: https://github.com/macmanes-lab/BinPacker/blob/master/README

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

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    Bridger

Cite this (Bridger, RRID:SCR_017039)

URL: https://github.com/fmaguire/Bridger_Assembler

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package as de novo trascriptome assembler for RNA-Seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

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Cite this (Discovar assembler, RRID:SCR_016755)

URL: https://software.broadinstitute.org/software/discovar/blog/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

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Cite this (NOVOPlasty, RRID:SCR_017335)

URL: https://github.com/ndierckx/NOVOPlasty

Resource Type: Resource, alignment software, image analysis software, data processing software, software resource, software application

Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data.

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    SHARCGS

Cite this (SHARCGS, RRID:SCR_002026)

URL: http://sharcgs.molgen.mpg.de/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.

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    SHORTY

Cite this (SHORTY, RRID:SCR_002048)

URL: http://www.cs.sunysb.edu/~skiena/shorty/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software for targeted de novo assembly of microreads with mate pair information and sequencing errors.

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Cite this (SplitSeek, RRID:SCR_001012)

URL: https://omictools.com/splitseek-tool

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

THIS RESOURCE IS NO LONGER SUPPORTED, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data.

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Cite this (Supernova assembler, RRID:SCR_016756)

URL: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software to generate phased, whole genome de novo assemblies from a Chromium prepared library. Used to create true diploid de novo assemblies and can separate homologous chromosomes over long distances.

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    Velvet

Cite this (Velvet, RRID:SCR_010755)

URL: http://www.molecularevolution.org/software/genomics/velvet

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux.

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    WTDBG

Cite this (WTDBG, RRID:SCR_017225)

URL: https://github.com/ruanjue/wtdbg2.git

Resource Type: Resource, image analysis software, data analysis software, data processing software, alignment software, software application, sequence analysis software, software resource

Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.

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