Results for "SPAdes"
Top-level pages
Genome Assembly Tools and Software - PART1 !!
...mbly based approach to detect genomic structural variations from whole-genome high-throughput sequencing datasets. SPAdes 3.6.2 – Single-cell Genome Assembler SPAdes (St. Petersburg genome assemb...2676 days ago
- ...umina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the ...squo;s group. Again, running spades.py will show you the options:...t> RAM limit for SPAdes in Gb (terminates if exceeded...
2342 days ago
- ...copy of duplicated lines: awk '!seen[$0]++' To sum assembly size from SPAdes contigs.fasta or scaffolds.fa...\tr "\t" "\n" > myf2.fq To filter and sort contig identifiers from SPAdes assembly (e.g. here lenght &g...
2208 days ago
Frequent parameters for bioinformatics tools !
...min_length 500 --min_mean_q 85 --min_window_q 65 FastQ Screen --aligner bowtie2' (bwa for PacBio) --subset 1000 (for PacBio) SPAdes --careful --disable-gzip-ou...1276 days ago
Short-read assembly using Spades !
...s, we could also assemble these using the tool Spades. You can try this here, or t...z: the Illumina reverse reads Assemble Run Spades: spades.py -1 illumina_R1....ina_R2.fastq.gz --careful --cov-cutoff auto -o spades_assembly_all_illumina...816 days ago
Bioinformatics tools for genome assembly !
...used genome assembly tools as of my last update in September 2021: SPAdes: An assembler specifically de...bler designed for long reads, particularly suited for PacBio data. SPAdes Long Read (SPAdesLR): An exte...277 days ago
Mitochondrial genome assembly tools !
...GetOrganelle can also be used for mitochondrial genome assembly. It is particularly useful for dealing with high-throughput sequencing data. SPAdes: SPAdes (St. Petersburg genome assemb...233 days ago
