Mercurial > repos > fangly > grinder

comparison grinder.xml @ 9:577e77853e8b

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Fixed a typo
author fangly
date Thu, 03 Nov 2011 23:58:59 -0400
parents 43def9fa33b9
children c9fee6113b0d
comparison
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8:43def9fa33b9 9:577e77853e8b
408 **What it does** 408 **What it does**
409 409
410 Grinder is a program to create random shotgun and amplicon sequence libraries 410 Grinder is a program to create random shotgun and amplicon sequence libraries
411 based on reference sequences in a FASTA file. Features include: 411 based on reference sequences in a FASTA file. Features include:
412 412
413 * omic support: genomic, metagenomic, transcriptomic, metatranscriptomic,
414 proteomic and metaproteomic
413 * shotgun library or amplicon library 415 * shotgun library or amplicon library
414 * arbitrary read length distribution and number of reads 416 * arbitrary read length distribution and number of reads
415 * simulation of PCR and sequencing errors (chimeras, point mutations, homopolymers) 417 * simulation of PCR and sequencing errors (chimeras, point mutations, homopolymers)
416 * support for creating paired-end (mate pair) datasets 418 * support for creating paired-end (mate pair) datasets
417 * specific rank-abundance settings or manually given abundance for each genome 419 * specific rank-abundance settings or manually given abundance for each genome
424 426
425 **Input** 427 **Input**
426 428
427 A variety of FASTA databases containing genes or genomes can be used as input 429 A variety of FASTA databases containing genes or genomes can be used as input
428 for Grinder, such as the NCBI RefSeq collection (ftp://ftp.ncbi.nih.gov/refseq/release/microbial/), 430 for Grinder, such as the NCBI RefSeq collection (ftp://ftp.ncbi.nih.gov/refseq/release/microbial/),
429 the GreenGenes 16S rRNA database (http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/Isolated_named_strains_16S_aligned.fasta), theh uman genome and transcriptome (ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/, ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz), ... 431 the GreenGenes 16S rRNA database (http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/Isolated_named_strains_16S_aligned.fasta), the human genome and transcriptome (ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/, ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz), ...
430 432
431 These input files can either be provided as a Galaxy dataset, or can be uploaded 433 These input files can either be provided as a Galaxy dataset, or can be uploaded
432 by Galaxy users in their history. 434 by Galaxy users in their history.
433 435
434 436