fastcat
A set of simply utilities for creating summaries from standard bioinformatics formats.
Installation
All tools are distributed in a single package from our conda channel, they can be installed into an isolated conda environment with:
mamba create -n fastcat -c conda-forge -c bioconda -c epi2melabs fastcat
Compilation
Although not recommended, compilation from source is via make:
make fastcat bamstats
Several libraries are assumed to be present on the system for linking.
fastcat
This eponymous tool concatenates .fastq(.gz) files whilst creating a summary of the sequences. Can also demultiplex reads according to Guppy/MinKNOW .fastq record headers.
Usage: fastcat [OPTION...] reads1.fastq(.gz) reads2.fastq(.gz) ...
fastcat -- concatenate and summarise .fastq(.gz) files.
-a, --min_length=MIN READ LENGTH
minimum read length to output (excluded reads
remain listed in summaries).
-b, --max_length=MAX READ LENGTH
maximum read length to output (excluded reads
remain listed in summaries).
-d, --demultiplex=OUT DIR Separate barcoded samples using fastq header
information. Option value is top-level output
directory.
-f, --file=FILE SUMMARY Per-file summary output
-q, --min_qscore=MIN READ QSCOROE
minimum read Qscore to output (excluded reads
remain listed in summaries).
-r, --read=READ SUMMARY Per-read summary output
-s, --sample=SAMPLE NAME Sample name (if given adds a 'sample_name'
column).
-x, --recurse Search directories recursively for '.fastq',
'.fq', '.fastq.gz', and '.fq.gz' files.
-?, --help Give this help list
--usage Give a short usage message
-V, --version Print program version
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
Input files may be given on stdin by specifing the input as '-'. When the -x
option is given inputs may be directories.
Report bugs to chris.wright@nanoporetech.com.
The program writes the input sequences to stdout in .fastq format to be
recompressed with gzip (or more usefully bgzip).
The per-read.txt is a tab-separated file with columns:
read_id filename read_length mean_quality
SRR12447496.1 SRR12447496_1.fastq.gz 531 14.03
SRR12447496.2 SRR12447496_1.fastq.gz 513 13.91
SRR12447496.3 SRR12447496_1.fastq.gz 473 14.70
...
The mean quality is defined as:
-10 * log10(mean(10^(Q/-10)))
where Q are the set of all per-base quality scores for the read.
The per-file.txt is also a tab-separated file with columns:
filename n_seqs n_bases min_length max_length mean_quality
SRR12447496_1.fastq.gz 16048 8090160 434 697 13.10
SRR12447498_1.fastq.gz 16203 8049713 421 697 13.25
SRR12447499_1.fastq.gz 15484 7812439 424 612 13.16
...
where the mean_quality column is the mean of the per-read mean_quality values.
bamstats
The bamstats utility is a re-implementation of the stats_from_bam program
from pomoxis. It creates read-level summary
statistics of alignments found in a BAM file and reports these in a TSV file.
Usage: bamstats [OPTION...] <reads.bam>
bamstats -- summarise rears/alignments in one or more BAM files.
General options:
-r, --region=chr:start-end Genomic region to process.
-t, --threads=THREADS Number of threads for BAM processing.
Read filtering options:
-g, --read_group=RG Only process reads from given read group.
--haplotype=VAL Only process reads from a given haplotype.
Equivalent to --tag_name HP --tag_value VAL.
--tag_name=TN Only process reads with a given tag (see
--tag_value).
--tag_value=VAL Only process reads with a given tag value.
-?, --help Give this help list
--usage Give a short usage message
-V, --version Print program version
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
The program creates a simple TSV file containing statistics for each primary
alignment stored within the input BAM files.
Report bugs to chris.wright@nanoporetech.com.
bamindex
The bamindex program is a rather curious program that will create a positional index
of alignments in a BAM file. It is intended to be used within workflows to allow
parallel processing of records in a BAM file, each worker processing a contiguous chunk
of the file. This is most useful with unaligned BAM files.
The program was insired by bri by Jared Simpson at OICR; which is far cooler.
There are three subcommands:
bamindex index
$ ./bamindex build --help
Usage: build [OPTION...] <reads.bam>
bamindex build -- create a BAM index corresponding to batches of records.
General options:
-c, --chunk_size=SIZE Number of records in a chunk.
-t, --threads=THREADS Number of threads for BAM processing.
-?, --help Give this help list
--usage Give a short usage message
-V, --version Print program version
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
The program creates a simple index of file offsets for each of every (n * M)th
alignment record. No care is taken to keep records corresponding to the same
query together, or any other such niceities. Its intended to be used simply
with unaligned, unsorted BAMs.
bamindex fetch
$ ./bamindex fetch --help
Usage: fetch [OPTION...] <reads.bam.bci>
bamindex fetch -- fetch records from a BAM according to an index.
General options:
-c, --chunk=SIZE Chunk index to retrieve.
-t, --threads=THREADS Number of threads for BAM processing.
-?, --help Give this help list
--usage Give a short usage message
-V, --version Print program version
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
The program simply will fetch a batch of records from a BAM fileusing and index
and a chunk ID.
bamindex dump
$ ./bamindex dump --help
Usage: dump [OPTION...] <reads.bam.bci>
bamindex dump -- dump a BAM chunk index to stdout as text.
-?, --help Give this help list
--usage Give a short usage message
-V, --version Print program version
The program simply writes the contents of an index to stdout for human
inspection. It has no other purpose.