String graph based genome assembly software and tools !
...transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate...2356 days ago
BBTools for bioinformatician !
...sition 19, zero-based). Code: $ kmercountexact.sh in=trimmed.fq out=counts.txt fastadump=f mincount=10 k=20 rcomp=f This will generate a file containing the counts of all 20-mers that occurred...2298 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an hist...2009 days ago
Qualimap2: Evaluating next generation sequencing alignment data
...l User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. Supported types of expe...2090 days ago
3893 days ago
Next generation sequencing in R or bioconductor environment
...nomial distribution. It expects as input a data frame with the raw read counts per region/gene of interest (...tial exon usage); parathyroidSE explains how to generate exon read counts in R DEGseq baySeq (also se...3652 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...https://github.com/warrenlr/LINKS/ Read clustering afcluster Clustering of reads from different genes and different species based on k-mer counts Software (C++) https://gith...2398 days ago
2102 days ago
Perl script to create a consensus of nucleotide sequences !
...sort {$b $a} map {length} @mi; # set w to the length of the longest element foreach my $j ( 0 .. $w-1 ){ # Initialize the base counts. my %h = ( a=>0, t=>...2059 days ago
1388 days ago
Comment on "Estimate Genome Size"
...ads2.fastq.gz | jellyfish count -m 31 -o fastq.counts -C -s 10000000000 -U 500 -t 3...# generate a histogram jellyfish histo fastq.counts_0 > fastq.counts_0.histo...inpoint the actual peak find_valleys.pl fastq.counts_0.histo # estimate the size...1925 days ago