How to inspect novoalign index

[blumroyParticipant]

We have generated a novoalign index file using the following command:
novoindex -k 14 -s 1 -t 8 -n mm10 mm10.ndx AllChroms.fa

After the mm10.ndx index file was generated, is there a way to inspect it in order to obtain the names of chromosomes included so to verify that the index is proper?

In Bowtie2 the parallel such query is achieved by running:
bowtie2-inspect -s mm10_ref

and the output would be, for example:
Flags 1
Reverse flags 5
Colorspace 0
2.0-compatible 1
SA-Sample 1 in 16
FTab-Chars 10
Sequence-1 chr1 195471971
Sequence-2 chr10 130694993
Sequence-3 chr11 122082543
Sequence-4 chr12 120129022
Sequence-5 chr13 120421639
Sequence-6 chr14 124902244
Sequence-7 chr15 104043685
Sequence-8 chr16 98207768
Sequence-9 chr17 94987271
Sequence-10 chr18 90702639
Sequence-11 chr19 61431566
Sequence-12 chr2 182113224
Sequence-13 chr3 160039680
Sequence-14 chr4 156508116
Sequence-15 chr5 151834684
Sequence-16 chr6 149736546
Sequence-17 chr7 145441459
Sequence-18 chr8 129401213
Sequence-19 chr9 124595110
Sequence-20 chrX 171031299
Sequence-21 chrY 91744698
Sequence-22 mtDNA 16299
Sequence-23 rDNA 248062

[Colin HercusKeymaster]

Hi,

For sure you can do this using novoutil.

Try novoutil headers mm10.ndx

Novoutil has some other functions that work with indexes..

novoutil sequence Can extract sequences (full or part) in fasta format.

novoutil index Checks index is valid and reports some build counts.

Colin

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