Results for "Scaffolds"
Blogs
Tools to detect synteny blocks regions among multiple genomes
.../download.html) MapSynteny is a macro in MS Excel® able to create images to show the relationship between genetic maps and large sequences (scaffolds, chromosomes, BACs, etc.). Ba...2604 days ago
String graph based genome assembly software and tools !
...errors in the reads. The second phase assembles contigs from the corrected reads. The third phase uses paired end and/or mate pair data to build scaffolds from the contigs. The output...2322 days ago
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Bookmarks
Alignment of closely related whole genomes/scaffolds
With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across th...3013 days ago
RACA: Reference-Assisted Chromosome Assembly
Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using com...2945 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
...liably order and orient sequence scaffolds generated by NGS and assemble...information is used to construct scaffolds that order and orient the con...cing reads and producing genomic scaffolds, open-reading frames and taxo...; Generate Draft Genome Sequence Scaffolds for ProkaryotesSIS (Scaf...2679 days ago
Top-level pages
Genome Assembly Tools and Software - PART1 !!
...red-end reads to connect repeat contigs into scaffolds, also provide the average cov...ol Scaffold_builder was designed to generate scaffolds (super contigs of sequences j...ly pipeline to automatically break incorrect scaffolds and flag other errors in an a...2679 days ago
Tools for bacterial whole genome annotation
...nd orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying...2325 days ago
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Wire posts
Bio-Scripts
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, load it, # if not, install and load it if("ggplot2" %in...2278 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script to see the distance beetween all the contigs and scaffolds #Usage: perl clustalReads.pl genome.fa >...2134 days ago
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Comments
Comment on "REAPR: a universal tool for genome assembly evaluation"
...reads. It is heavily based on too low span coverage, or reads mapping too far or too close to each other. The program will also break up contigs/scaffolds at spurious sites to form sma...1331 days ago
Comment on "Perl script to count number of Ns in a multifasta file !"
...fasta file. (base) ? output_2_test git:(master) ? more scaffolds.fasta | grep -Ho N * | uniq -c 12 draft_summary.info:N 1035948 scaffolds.fasta:N ...1557 days ago
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