Results for "de-novo assembly"
Top-level pages
When you have both Illumina and Nanop...ains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s g....fastq \ -o hybrid_assembly In turn, these parameter...utput in folder “hybrid_assembly”...2343 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the...ng the quality of genome assemblies created via an assembly software. PAGIT compiled four...tware pipeline for high-quality prokaryotic genome assembly and annotation. It was valida...2324 days ago
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembl...typically by minimap) as input and outputs an assembly graph in the GFA fo...> AONT_miniasm_self10000.eps Njoy the assembly !...2322 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing final results but also for impro...pplication that uses a novel graph-based representation to display a sequence assembly and associated metadata http...2276 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...2266 days ago
Some useful Bioinformatics links
...hub.com/GATB/DiscoSnp De novo assembly | Oxford Nanopore Technologie...my/term/131 De novo long-read assembly of a complex animal genome |...//github.com/nanoporetech/ont-assembly-polish Generade-nl/TULIP: TUL...du/Disco SAGE: String-overlap Assembly of GEnomes | BMC Bioinformati...2234 days ago
- To remove all line ends (\n) from a Unix text file: sed '...py of duplicated lines: awk '!seen[$0]++' To sum assembly size from SPAdes contigs.fast...To filter and sort contig identifiers from SPAdes assembly (e.g. here lenght >= 4000...
2210 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling...s, for example "GapFiller: a de novo assembly approach to fill the gap with...orithm: 1. Start with the initial assembly C0 of the contigs you have id...aired-end reads. c. Construct a new assembly C' from C and the new reads i...2157 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ &&...2174 days ago
My commonly used commands in Bioinformatics
FYI, I've found it useful to use MUMmer to extract the spe...o 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...2102 days ago
