Welcome to


The toolkit for assessing long read sequencing data.



Look here and here for sample reports

Download

Get the source code from here, or type

git clone https://github.com/grabherr/InSeqt.git

in a terminal window.


Build

cd into your local directory (cd Inseqt) and type make.


Run

The main executable is run like so:
./InSeqt
This will list all available options.
Run ./InSeqt [command] to see the options of each individual command.

InSeqt basic

To get a quick and basic idea of what the fundamentals of the data look like, run

BasicStats -i <file_or_list> -o <output_dir> > out

where you either provide a single fastq file, or a list of files, with one entry per line. Follow this up by

cd <output_dir>
./InSeqt report -i ../out

and it will generate an HTML file with basic statistics, length and GC distribution etc.

InSeqt lapcands

To first generate a list of read-read overlap candidates, run multiple instances of

FindOverlapCands -i <input> -o <outfile> -c <chunks> -n <chunkindex> -f <fraction>

where -c specifies how many chunks you process (equals the number of instances you run), -n the index of the chunk, and -f the fraction of reads - as an absolute value, not a percentage. For example, to analyze a set of overlaps using 5 processes on 1% of the data, run

FindOverlapCands -i <input> -o <outfile> -c 5 -n 0 -f 0.01 > overlaps0 &
FindOverlapCands -i <input> -o <outfile> -c 5 -n 1 -f 0.01 > overlaps1 &
FindOverlapCands -i <input> -o <outfile> -c 5 -n 2 -f 0.01 > overlaps2 &
FindOverlapCands -i <input> -o <outfile> -c 5 -n 3 -f 0.01 > overlaps3 &
FindOverlapCands -i <input> -o <outfile> -c 5 -n 4 -f 0.01 > overlaps4 &

Once done, concatenate the overlaps:

cat overlaps* > all_overlaps

To get a distribution of overlaps, run:

LapStats -i all_overlaps -r overlaps0.allreadnames -o <output_dir>