BOL: Results for "Assembly"

Comment on "Short-read assembly using Spades !" by BioStar

Fri, 17 Mar 2023 00:17:37 -0500

...software tool for short-read assembly. Here are the general steps for short-read assembly using SPAdes: Quality co...TQ format. Evaluation of assembly: After running SPAdes, the ne...repeated until a satisfactory assembly is achieved. These are t...

Comment on "Short-read assembly using Spades !" by LEGE

Sat, 11 Mar 2023 13:43:19 -0600

...e assembler) is a popular tool for short-read assembly. It can assemble reads genera...overview of how to use SPAdes for short-read assembly: Install SPAdes: SPAdes...also provides several options for tuning the assembly parameters, such as adjusting...

Comment on "Run miniasm assembler on nanopore reads !" by Rahul Nayak

Tue, 01 Mar 2022 03:21:40 -0600

..../minimap.paf.gz > miniasm.gfa awk ’/^S/{print “>”$2”\n”$3}’ miniasm.gfa > miniasm.fasta assembly-stats ./miniasm.fasta dnadif...

Comment on "Genome assembly training tutorial at Galaxy !" by Neel

Sat, 25 Sep 2021 10:21:46 -0500

Understandinng genome assembly processes https://academic.oup.com/bfg/article/15/1/1/1741842

Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies" by Neel

Sun, 06 Sep 2020 10:19:23 -0500

...) – we can plot the kmer content of the assembly compared to the kmer content...comparison between the combined reads and the assembly. Make sure that you use the f...kmer “noise” is part of the final assembly? What do you think contamina...

Comment on "REAPR: a universal tool for genome assembly evaluation" by Neel

Sun, 06 Sep 2020 10:17:23 -0500

...g to find explicit errors in the assembly based on incongruently mapped...e command reapr facheck <assembly.fasta> will tell you...lems, run reapr facheck <assembly.fasta> assembly.fa. Use this file together wi...

Comment on "Tools to detect synteny blocks regions among multiple genomes" by Neel

Tue, 09 Jun 2020 20:15:15 -0500

Synteny based tool to arrange contigs "r2cat: synteny plots and comparative assembly" http://bibiserv.techfak.uni-bielefeld.de/r2cat https://academic.oup.com/bioinformatics/article/26/4/570/243369

Comment on "Genome assembly tutorial "Genome Assembly for short and long reads"" by Jit

Tue, 25 Feb 2020 03:21:18 -0600

Do it yourself guide to genome assembly https://academic.oup.com/bfg/article/15/1/1/1741842

Comment on "Bioinformatics tools developed for Oxford Nanopore data analysis !" by Rahul Nayak

Thu, 06 Feb 2020 23:29:18 -0600

Basic commands for genome assembly https://raw.githubusercontent.com/rrwick/Long-read-assembler-comparison/master/supplementary_figures/Fig_S04_commands.png

Comment on "RGFA: powerful and convenient handling of assembly graphs" by Rahul Nayak

Mon, 20 Jan 2020 05:39:22 -0600

The Graphical Fragment Assembly (GFA) is a proposed format which allow to describe the product of sequence assembly. This gem implements the proposed specifications for the GFA format described under https://github.com/GFA-spec/GFA-spec/blob/master/GFA-spec.md as close as possible.