This takes a query sequence and a blast database built with the atram_preprocessor.py script and builds assemblies.
If you specify more than one query sequence and/or more than one blast database then aTRAM will build one assembly for each query/blast DB pair.
NOTE: You may use a text file to hold the command-line arguments like: @/path/to/args.txt. This is particularly useful when specifying multiple blast databases or multiple query sequences.
-h, --help
Show this help message and exit.
--version
Show program's version number and exit.
-b DB [DB ...], --blast-db DB [DB ...], --sra DB [DB ...], --db DB [DB ...], --database DB [DB ...]
This needs to match the DB prefix you entered for atram_preprocessor.py. You may repeat this argument to run the --query sequence(s) against multiple blast databases.
-q QUERY [QUERY ...], --query QUERY [QUERY ...], --target QUERY [QUERY ...], --probe QUERY [QUERY ...]
The path to the fasta file with sequences of interest. You may repeat this argument. If you do then Each --query sequence file will be run against every --blast-db.
-Q QUERY_SPLIT [QUERY_SPLIT ...], --query-split QUERY_SPLIT [QUERY_SPLIT ...], --target-split QUERY_SPLIT [QUERY_SPLIT ...]
The path to the fasta file with multiple sequences of
interest. This will take every sequence in the fasta
file and treat it as if it were its own --query
argument. So every sequence in --query-split will be
run against every --blast-db.
-o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
This is the prefix of all of the output files. So you can identify different blast output file sets. You may include a directory as part of the prefix. aTRAM will add suffixes to differentiate output files.
-a {abyss,trinity,velvet,spades,none}, --assembler {abyss,trinity,velvet,spades,none}
Which assembler to use. Choosing "none" (the default) will do a single blast run and stop before any assembly.
-i N, --iterations N
The number of pipeline iterations. The default is "5".
-p, --protein
Are the query sequences protein? aTRAM will guess if you skip this argument.
--fraction FRACTION
Use only the specified fraction of the aTRAM database. The default is 1.0.
--cpus CPUS, --processes CPUS, --max-processes CPUS
Number of CPU processors to use. This will also be used for the assemblers when possible. We will use 8 out of 12 CPUs.
--log-file LOG_FILE
Log file (full path)".
--path PATH
If the assembler or blast you want to use is not in your $PATH then use this to prepend directories to your path.
-t DIR, --temp-dir DIR
Place temporary files in this directory. All files will be deleted after aTRAM completes. The directory must exist.
--keep-temp-dir
This flag will keep the temporary files in the --temp-dir around for debugging.
-T SECONDS, --timeout SECONDS
How many seconds to wait for an assembler before stopping the run. To wait forever set this to 0. The default is "300" (5 minutes).
--no-filter
Do not filter the assembled contigs. This will: set both the --bit-score and --contig-length to 0
--bit-score SCORE
Remove contigs that have a value less than this. The default is "70.0". This is turned off by the --no- filter argument.
--contig-length CONTIG_LENGTH, --length CONTIG_LENGTH
Remove blast hits that are shorter than this length. The default is "100". This is turned off by the --no- filter argument.
--db-gencode CODE
The genetic code to use during blast runs. The default is "1".
--evalue EVALUE
The default evalue is "1e-10".
--word-size WORD_SIZE
Word size for wordfinder algorithm. 'Must be >= 2.
--max-target-seqs MAX
Maximum hit sequences per shard. Default is calculated based on the available memory and the number of shards.
--batch-size BATCH_SIZE
Use this option to control blast memory usage and the concatenation of queries. Setting this value too low can degrade performance.
--no-long-reads
Do not use long reads during assembly. (Abyss, Trinity, Velvet)
--kmer KMER
k-mer size. The default is 64 for Abyss and 31 for Velvet. Note: the maximum kmer length for Velvet is 31. (Abyss, Velvet)
--mpi
Use MPI for this assembler. The assembler 'must have been compiled to use MPI. (Abyss)
--bowtie2
Use bowtie2 during assembly. (Trinity)
--max-memory MEMORY
Maximum amount of memory to use in gigabytes. We will use 12 out of 24 GB of free/unused memory. (Trinity, Spades)
--exp-coverage EXP_COVERAGE, --expected-coverage EXP_COVERAGE
The expected coverage of the region. The default is "30". (Velvet)
--ins-length INS_LENGTH
The size of the fragments used in the short-read library. The default is "300". (Velvet)
--min-contig-length MIN_CONTIG_LENGTH
The minimum contig length used by the assembler itself. The default is "100". (Velvet)
--cov-cutoff COV_CUTOFF
Read coverage cutoff value. Must be a positive float value, or "auto", or "off". The default is "off". (Spades)