Quality control

Compute statistics

amo base_call \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_FAST5_FILE> \
-type 0 \
-output [OUTPUT_DIRECTORY]

amo atgc_stats \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_FASTQ_FILE> \
-output [OUTPUT_DIRECTORY]

Quality control

amo atgc_quality \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_ZIP_FILE> \ # e.g., seqkit-benchmark-data.tar.gz
-output [OUTPUT_DIRECTORY]

Filter reads

amo read_filter \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_ZIP_FILE> \ # e.g., test_quality.fastq.gz
-output [OUTPUT_DIRECTORY]

Assembly using DeBrujin Graph

amo atgc_assembly \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_FASTQ_FILE> \ # e.g., test_assembly.fastq
-type 0 \
-kmer 5 \
-output [OUTPUT_DIRECTORY]

Assembly using Swarm-intelligence

amo atgc_assembly \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_FASTQ_FILE> \ # e.g., test_assembly.fastq
-type 1 \
-kmer 5 \
-output [OUTPUT_DIRECTORY]

Correction

amo atgc_correct \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_FASTQ_FILE> \
-output [OUTPUT_DIRECTORY]

Gene expression

Coming soon ...

Kmer counter

amo kmer_counter \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_FASTQ_FILE> \ # e.g., fastq_runid_c2d19c211888bc09d8e077df271f325c911c1010_0.fastq \
-output [OUTPUT_DIRECTORY]

Kmer generator

amo kmer_generator \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_FASTQ_FILE> \ # e.g., fastq_runid_c2d19c211888bc09d8e077df271f325c911c1010_0.fastq \
-min 1 \
-output [OUTPUT_DIRECTORY]