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Database URL Description Short variations—SNVs, short indels 1000 Genomes http://www.1000genomes.org Human short variants and inferred genotypes dbSNP http://www.ncbi.nlm.nih.gov/projects/SNP Short variants from all species HapMap http://www.hapmap.org Human short variants […] http://code.google.com/p/ea-utils/
Primarily written to support an Illumina based pipeline – but should work with any FASTQs. Overview: fastq-mcf Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering. fastq-multx Demultiplexes a fastq. Capable of auto-determining barcode […] An approximate workflow for repeating the phylogenetic analysis of strawberry and other plant genomes would consist of the following steps: 1) Obtain protein and nucleotide sets from the identified sources. Extract subregions of protein and nucleotide sequences specified in the gene identifiers spreadsheet and group into files by family. 2) Search nucleotide sequences for papaya […] ELPH : Estimated Locations of Pattern Hits Overview ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, […] Next Generation Sequencing (NGS) is a frequently applied approach to detect sequence variationsbetween highly related genomes. Recent large-scale re-sequencing studies as the Human 1000 GenomesProject utilize NGS data of low coverage to afford sequencing of hundreds of individuals. Here, SNPsand micro-indels can be detected by applying an alignment-consensus approach. However,computational methods capable of […] Description ANNOVA is an efficient software tool to utilize update-to-date information to functionally annotategenetic variants detected from diverse genomes. Given a list of variants with chromosome, startposition, end position and observed nucleotides, ANNOVAR can identify whether SNPs or indels causeprotein coding changes and what is the amino acids that were changed, or identify variants […] http://abacas.sourceforge.net/index.html ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.
ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output is then processed to generate a pseudomolecule taking overlapping […] ABBA From amos Jump to: navigation, search ABBA: Assembly Boosted By Amino acid sequences Contents [hide] 1 Overview 2 Download 3 References 4 Acknowledgements Overview Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper. […] samtools mpileup -uf ref.fa aln.bam | bcftools view -cg – | vcfutils.pl vcf2fq > cns.fq |
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