degap_align.py --help
usage: degap_align.py [-h] -f FASTA [--debug]
Removes gap-only columns from an aligned fasta file, thus maintaining the
alignment.
optional arguments:
-h, --help show this help message and exit
-f FASTA, --fasta FASTA
FASTA file
--debug
simply counts the number of sequences in a fasta or fastq file. .gz endings are supported.
fastcount FILENAME
fastfilter --help
usage: fastfilter [-h] [-q QUERY | -f FILTERFILE] [-r] [-g] [-l LENGTH]
[--fasta] [-v]
FILE
Filters sequences (inclusive or exclusive) from a file (fasta or fastq) using
either pattern matching of the ID line or sequence lengths.
positional arguments:
FILE fasta or fastq file to search (may be gzipped if
suffix = .gz)
optional arguments:
-h, --help show this help message and exit
-q QUERY, --query QUERY
search term
-f FILTERFILE, --filterfile FILTERFILE
file with list of query terms
-r, --reverse removes records with given terms (reverse of default
behavior)
-g, --grep grep matching of query term (default is exact match)
-l LENGTH, --length LENGTH
length range, specified like 100-200 or -200 or 200-
--fasta output sequences as fasta (even if fastq input)
-v, --verbose increase output verbosity
flash_overlap.py --help
usage: flash_overlap.py [-h] file1 file2 flash
Calculates the overlap in flash-joined reads
positional arguments:
file1 fastq file (input to flash)
file2 fastq file (input to flash)
flash flash output
optional arguments:
-h, --help show this help message and exit
- required perl5 libs: TryCatch, Bio::Tools::GFF
gffliftover.pl
Usage:
gffliftover.pl -f alignment.fasta -g annotation.gff [-v
input_gff_version] [-help] [-debug]
Required arguments:
-f Aligned fasta file (includes the reference and at least 1 additional sequence)
-g Reference gff file
Options:
-v GFF file version (default is 3)
-help -h Help