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sequencetools

Set of scripts etc. to work with DNA sequence and related files:

assemblathon_stats.pl

Basic statistics on contigs and scaffolds. Modifed after https://github.com/ucdavis-bioinformatics/assemblathon2-analysis

scaffoldgap2bed.py

Generates a bed-file for the gaps or contigs for a given fasta file Splits the sequences on gaps of (default): 20 bases. Requires BioPython.

Example in IGV of a short sequence with a track for gaps and contigs from bedfiles generated by the script:

trf2gff.py

Converts the output from the TRF program (http://tandem.bu.edu/trf/trf.html) to a gff file Requires the -ngs flag set (available from TRF version 4.07b). Really rough code, use at your own risk Usage:

python trf2gff.py trf_outfile.dat >trf_outfile.gff

fasta_length

Returns the length of each fasta entry, one length per line of output Usage:

fasta_length sequences.fasta

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Set of scripts etc. to work with DNA sequence and related files

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