Pinned Repositories
chex-analysis
This repository contains code for CHEX-seq data analysis.
chex-seq
This is the computational pipeline for CHEX-seq data
smito-analysis
This repository contains code for SMITO data analysis
smito-pipeline
Single-MITOchondrion (SMITO) SNV Pipeline
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_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).
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
luyoutao's Repositories
luyoutao/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).
luyoutao/fa_baseviz
Visualize FATSA/FASTQ to reveal primer/adaptor pattern
luyoutao/fa_seq_compressibility
From FASTA calculates sequence compressibility in fixed-sized windows
luyoutao/office
snippets for system admin & doc automation
luyoutao/sam_cigarmd_split
Split query sequence and phred scores into softclip (S), insertion (I), match (=) and mismatch (X) according to CIGAR and tag MD.
luyoutao/sam_insertsize_stats
Calculate summary stats for insert sizes (TLEN) for BAM/SAM
luyoutao/sam_mappedLength_mismatches
Calculate the nonoverlapping mapped length and the number of mismatches per read pair and per mate (if tag NM available)
luyoutao/sam_seq_compressibility
Calculate sequence complexity per read (pair) from SAM or BAM
luyoutao/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.
luyoutao/sam_subsample
Random sample --num reads (SE) or read pairs (PE) from BAM or SAM
luyoutao/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.