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on page 1 showing 4 out of 4 results

    BWA

Cite this (BWA, RRID:SCR_010910)

URL: http://bio-bwa.sourceforge.net/

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

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: one for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

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    FLASH

Cite this (FLASH, RRID:SCR_005531)

URL: http://ccb.jhu.edu/software/FLASH/

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

Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.

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Cite this (Trimmomatic, RRID:SCR_011848)

URL: http://www.usadellab.org/cms/index.php?page=trimmomatic

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

Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.

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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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