Update README with new dependencies introduced in 2.0.3

[mmokrejs]

The 2.0.3 release now optionally depends on pigz (I am assuming http://www.zlib.net/pigz/) and zsh (do you really mean https://www.zsh.org ?).

Has the documentation been updated to cope with the following change?

abyss-pe:
    Fix: use N instead of n for scaffold stage, when set by user

I shall hopefully soon dive into this and would like to avoid using wrong/changed variablenames.

This minor release provides bug fixes and improved reliability for both MPI assemblies and Bloom filter assemblies on large datasets. In addition, many usability improvements have been made to the abyss-samtobreak program for miasssembly assessment.

overall:

    Many compiler fixes for GCC >= 6, Boost >= 1.64
    Read and write GFA 2 assembly graphs with abyss-pe graph=gfa2
    Support reading CRAM via samtools

abyss-bloom:

    New abyss-bloom build -t rolling-hash option, to
    pre-build input Bloom filters for abyss-bloom-dbg
    Fix incorrect output of abyss-bloom kmers -r
    (thanks to @notestaff!)

abyss-bloom-dbg:

    New -i option to read Bloom filter files built by
    abyss-bloom build -t rolling-hash
    Improved error branch trimming (reduces number of
    small output sequences)
    Fix intermittent segfaults caused by non-null-terminated
    strings

abyss-map:

    Append BX tag to SAM output (Chromium 10x Genomics data)

ABYSS-P:

    Increase default number of sparsehash buckets from
    200,000,000 => 1,000,000,000
    Benefit: Allows larger datasets to be assembled without
    time-consuming sparsehash resize operations (e.g. H. sapiens)
    Caveat: Increases minimum memory requirement per
    CPU core from 89 MB to 358 MB

abyss-pe:

    Parallelize gzip with pigz, if available
    Report time/memory for each program with zsh, if available
    Fix: use N instead of n for scaffold stage,
    when set by user

abyss-samtobreak:

    New --alignment-length (-a) option to exclude alignments
    shorter than a given length
    New --contig-length (-l) option to exclude contigs
    shorter than a given length
    New --genome-size (-G) option, for contiguity metrics
    that depend on the reference genome size
    New --mapq (-q) option for minimum MAPQ score
    New --patch-gaps (-g) option to join alignments
    separated by small gaps
    New TSV output format with additional contiguity
    stats (e.g. L50, NG50)
    Fix handling of hard-clipped alignments

abyss-todot:

    New --add-complements option

abyss-tofastq:

    New --bx option to copy BX tag from from SAM/BAM
    to FASTQ header comment (Chromium 10x Genomics
    data)

[sjackman]

Do you really mean https://www.zsh.org ?

Yes. See https://github.com/bcgsc/abyss/blob/578d094ba065e6c950cd0e2cb04c45c5b95f83c8/bin/abyss-pe#L9

[sjackman]

Has the documentation been updated to cope with the following change?

abyss-pe: Fix: use N instead of n for scaffold stage, when set by user

This is a bug fix to bring the code in line with the documentation. No change is needed for the documentation.

[sjackman]

I've added this text.

Optional dependencies

• pigz for parallel gzip
• samtools for reading BAM files
• zsh for reporting time and memory usage

[benvvalk]

Thanks, @sjackman!

[mmokrejs]

Thank you for the above commits. Provided samtools changed commandline syntax, I assume samtools-1.x is required and not samtools-0.x. Am I right? I would prefer stating minimal versions of boost and samttols, though.

I shall test the SAM to BAM conversion soon using samtools-1.5 soon.

[sjackman]

The SAM/BAM support in abyss-pe has been around for quite a while, prior to samtools 1.x, so it may support both 0.x and 1.x. (I don't know for certain.) I don't know what the minimum version of Boost is, but it's probably about 8 years old, from when ABySS was created.