Results for "Contigs"
Top-level pages
...ioinformatics tools are necessary to arrive from a raw DNA sequence at an annotated protein sequences: establish the correct order of sequence contigs to obtain one continuous sequ...3941 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...ign without available reference. Willing et al., Bioinformatics 27(16):2187-93, 2011. Publisher Website Local de novo assembly of RAD paired-end contigs using short sequencing reads....3773 days ago
Commercial and public next-gen-seq (NGS) software
...Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly. Includes SNP..., 454, ilumina), parse caf, ace and bowtie map files, clean and filter contigs, look for snps and indels., f...3512 days ago
Software packages for next gen sequence analysis
...e assembly of Illumina, SOLiD and Roche FLX data. Uses a novel Condensation Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly. Includes SNP...3236 days ago
Genome Assembly Tools and Software - PART1 !!
...[2] to extend seed reads (or contigs generated by another assembler) into longer contigs, by iteratively calling Vmatc...for analyzing ABySS-assembled contigs from shotgun transcriptome da...short read assembly (a set of contigs), a set of related references...2679 days ago
- ...file with PacBio reads --nanopore <filename> file with Nanopore reads --tslr <filename> file with TSLR-contigs --trusted-contigs <filename> f...
2344 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsystems in the SEED d...s: (i) ABACAS which classifies and orientates contigs and estimates the sizes of ga...m; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the sca...2325 days ago
Some useful Bioinformatics links
...lp.bioiplug.com/tetra-nucleotide-analysis-tna/ Clustering metagenomic contigs on tetranucleotide frequency...documentation http://cgat.readthedocs.io/en/latest/recipes/metagenome_contigs_kmers.html2235 days ago
- ...a in *.fasta; do ls $a; grep "^>" -c $a; done To keep only one copy of duplicated lines: awk '!seen[$0]++' To sum assembly size from SPAdes contigs.fasta or scaffolds.fasta file...
2211 days ago
- ...triggers for libc-bin (2.23-0ubuntu10) ...➜ redundans git:(master) ✗ python2 redundans.py -v -i test/*_?.fq.gz -f test/contigs.fa -o test/run1Options: Namespace(fasta='test/contigs.fa', fastq=['test/5000_1.fq.g...
2184 days ago
