1597 days ago
Installing ggplot2 and its dependencies on Ubuntu !
...ent type 'application/x-gzip' length 394424 bytes (385 KB) ======...ent type 'application/x-gzip' length 368081 bytes (359 KB) ======...D_FORTIFY_SOURCE=2 -g -c stri_length.cpp -o stri_length.o g++ -st...U_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg...1594 days ago
Python script to check sequence length in multifasta file
#!/usr/bin/python from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)1259 days ago
Reformat the multifasta for sequence length !
#awk oneliner to reformat the multifasta sequences awk '!/^>/ {printf "%s", $0; n = "\n"} /^>/ {print n $0; n = ""}' file.fasta | fold -w 1001436 days ago
Bash script to handle Multifasta files
...t.fasta > output.fasta #Rearrange FASTA sequences according to their length $ awk '/^>/ {printf("%s%s\...} END {printf("\n");}' input.fasta |\ >awk -F '\t' '{printf("%d\t%s\n",length($2),$0;)}' |\ >sort -k1,1n |...1401 days ago
1384 days ago
1259 days ago
Commandline for paired end reads simulation with BBMap !
....fq paired interleaved reads=100k length=250 mininsert=400 maxinsert=6....fq paired interleaved reads=100k length=250 mininsert=400 maxinsert=6...paired, interleaved, reads=100k, length=250, mininsert=400, maxinsert...CE_NOREF=false paired=true read length=250 reads=100000 insert siz...1034 days ago
Tadpole is 250x faster than SPADes assembler !
...ct reads. Tadpole has no upper bound for kmer length, but some values are not sup...Hashing parameters: k=31 Kmer length (1 to infinity). Memory use...read ends. window=12 (w) Length of window to use in reassembl...1020 days ago
Perl script for Smith-Waterman Algorithm
# Smith-Waterman Algorithm # usage statement die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2) = @ARGV; # scoring s...994 days ago