Results for "Assembly"
Top-level pages
Tools for bacterial whole genome annotation
...toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four...AS). MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was valida...2315 days ago
Run miniasm assembler on nanopore reads !
...read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA fo...ONT_miniasm_self.paf > AONT_miniasm_self10000.eps Njoy the assembly !2314 days ago
List of visualization tools for genome alignments
... interpretation of results: ABySS Explorer Interactive Java application that uses a novel graph-based representation to display a sequence assembly and associated metadata http...2268 days ago
Computational resources for TE discovery and TE detection
Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in deve...2258 days ago
Some useful Bioinformatics links
...github.com/GATB/DiscoSnp De novo assembly | Oxford Nanopore Technologie...onomy/term/131 De novo long-read assembly of a complex animal genome |...ps://github.com/nanoporetech/ont-assembly-polish Generade-nl/TULIP: TUL...s-odu/Disco SAGE: String-overlap Assembly of GEnomes | BMC Bioinformati...2225 days ago
- ...To keep only one copy of duplicated lines: awk '!seen[$0]++' To sum assembly size from SPAdes contigs.fast..."\n" > myf2.fq To filter and sort contig identifiers from SPAdes assembly (e.g. here lenght >= 4000...
2201 days ago
Gap filling or Contigs extensions tools !
...hort reads, for example "GapFiller: a de novo assembly approach to fill the gap with...owing algorithm: 1. Start with the initial assembly C0 of the contigs you have id...ese new paired-end reads. c. Construct a new assembly C' from C and the new reads i...2149 days ago
My commonly used commands in Bioinformatics
...that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta n...2094 days ago
Short-read assembly using Spades !
...llumina reverse reads Assemble Run Spades: spades.py -1 illumina_R1.fastq.gz -2 illumina_R2.fastq.gz --careful --cov-cutoff auto -o spades_assembly_all_illumina -1 i...809 days ago
Bioinformatics tools for genome assembly !
There are numerous genome assembly tools available, each with its st...a list of some widely used genome assembly tools as of my last update in...ads for circular bacterial genome assembly. wtdbg2: A de Bruijn gra...s is constantly evolving, and new assembly tools may have emerged since...270 days ago
