2669 days ago
String graph based genome assembly software and tools !
...reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended t...2467 days ago
3090 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
...hierachical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences As...3053 days ago
Bio++ : C Language libraries for your biological need
...emical distance (Miyata and Grantham) + import from any AAIndex entry.Consensus sequences.Pairwise alignment....hm).Mixed distance/ML tree reconstruction (iterative approaches).Tree consensus methods, bipartitions, bootst...4086 days ago
Genome Assembly Tools and Software - PART2 !!
...Illumina PCR-free fragment reads. SeqCons 1.0 – de novo and reference-guided Sequence Assembly SeqCons (Sequence consensus) is an open source consensus computation program for Linux...2824 days ago
List of In-silico Binding Site Prediction Tools
...ased drug design. Many computational methods for the prediction of ligand-binding sites have been developed in recent decades. Here we present a consensus method metaPocket, in which t...3882 days ago
Next generation sequencing in R or bioconductor environment
...owing sample code uses the test data set from the above BayesPeak package in order to compare the results from both methods by identifying their consensus peak set. Documentation [ Pub...3763 days ago
2510 days ago
4011 days ago
Create genome scaffolding with Perl
...return(scalar(reverse($seq))); } sub getConsensus { my ($b1, $b2) = @_; i...)){ ## equal bases, or absent bases, so consensus is easy return($b1);...lacementSeqs{$sName}{score}) && ($consensusLength > $replacementSeqs{$sNa...2447 days ago
Perl script to create a consensus of nucleotide sequences !
...warnings; my @instances = qw ( AAAAA ATCGA ATAAA ); my @instances2 = qw ( AAAAA AACGA ATAAA AGAAA AGAAA); print consensus(@instances),"\n"; # ATAAA print consensus(@instances2),"\n"; # AT...2170 days ago
Comment on "Nanopolis: polish a genome assembly"
...mtools index reads.sorted.bam python nanopolish_makerange.py draft.fa | parallel --results nanopolish.results -P 8 \ nanopolish variants --consensus -o polished.{1}.vcf -w {1} -r...2238 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...ds) Minimap and miniasm are ultrafast tools for (i) mapping and (ii) assembly. Designed for long, noisy reads, they do not have a correction or consensus step, and therefore the resul...2314 days ago