luyoutao's repositories
sam_best_hits
Compare primary alignment scores from several SAM/BAM files. For each read (read pair if paired-end [PE]), output score from the respective input (blank if absent) as well as which one has the best score (multiple if ties).
fa_baseviz
Visualize FATSA/FASTQ to reveal primer/adaptor pattern
fa_seq_compressibility
From FASTA calculates sequence compressibility in fixed-sized windows
office
snippets for system admin & doc automation
sam_cigarmd_split
Split query sequence and phred scores into softclip (S), insertion (I), match (=) and mismatch (X) according to CIGAR and tag MD.
sam_insertsize_stats
Calculate summary stats for insert sizes (TLEN) for BAM/SAM
sam_mappedLength_mismatches
Calculate the nonoverlapping mapped length and the number of mismatches per read pair and per mate (if tag NM available)
sam_seq_compressibility
Calculate sequence complexity per read (pair) from SAM or BAM
sam_is_sorted
Test whether a SAM/BAM is coordinate/queryname sorted. It outputs 'true' if sorted, 'false' if not, and 'unknown' if cannot decide.
sam_subsample
Random sample --num reads (SE) or read pairs (PE) from BAM or SAM
ukk
Given a query string (length n) and a pattern (length m), output all matches including inexact matches (cost k). This extends the original Ukkonen's algorithm (O(min(m, n)*k) complexity) but allows partial matches at the 5' or 3' end and mismatches under given error rate.