HIV Analysis in Galaxy: A high level plan

nekrut commented 6 years ago

Two main data generation strategies: (1) amplicon sequencing and (2) shotgun sequencing
At this time analysis one can choose calling variants or performing within-host evolution analyses including selection detection, rate of evolution, various types of temporal and spatial dynamic analyses. These begin with the following general themes:
Shotgun data can be analyzed either "read-by-read" using individual reads (i.e., Neher's sliding window approaches) or by reconstructing individual haplotypes.
There is a number of haplotype reconstruction approaches (nice summary of various approaches is in the introduction section of SAVAGE paper ). Two practical (based on perceived software availability) approaches are:
1. SAVAGE - overlap graph-based approach. There is a conda recipe for Linux. However it is unusable due to boost versioning. Need to check scalability on large number of reads.
2. ShoRAH - uses read alignments to a reference genome to reconstruct local haplotypes and then use these to reconstruct global (genome-wide) haplotypes. No conda package. Minimal documentation.
  - Once haplotypes are generates multiple alignments are generated with something like MAFFT.
  - Tree reconstruction can then be performed with tools such as RAxML or IQTree.
  - The subsequent analyses are based on multiple datamonkey tools (such as RELAX) and HyPhy.

Separately we want to implement tools for metagenomic identification of viral sequences along the lines of this paper.

davebx commented 6 years ago

Meeting 2018-10-16 tasks

[x] Create nexus/fasta datatype
[x] Finish the GARD wrapper
[x] Finish the MEME wrapper

davebx commented 6 years ago

Upcoming work per 2018-10-23 meeting:

[ ] Create or update SAVAGE bioconda recipe
[ ] Create or update ShoRAH bioconda recipe

nekrut commented 6 years ago

There are the following issues with Shorah and Savage:

SHOrah seems to lack `libopenblas.so.0`:

 amplian.py -b  ~/git/shorah/examples/amplicon_test/ampli_sorted.bam -f ~/git/shorah/examples/amplicon_test/reference.fasta -m 0.95
/home/anton/miniconda3/envs/shorah/bin/diri_sampler: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
--- Logging error ---
Traceback (most recent call last):
  File "/home/anton/miniconda3/envs/shorah/lib/python3.5/logging/handlers.py", line 71, in emit
    if self.shouldRollover(record):
  File "/home/anton/miniconda3/envs/shorah/lib/python3.5/logging/handlers.py", line 187, in shouldRollover
    msg = "%s\n" % self.format(record)
  File "/home/anton/miniconda3/envs/shorah/lib/python3.5/logging/__init__.py", line 836, in format
    return fmt.format(record)
  File "/home/anton/miniconda3/envs/shorah/lib/python3.5/logging/__init__.py", line 573, in format
    record.message = record.getMessage()
  File "/home/anton/miniconda3/envs/shorah/lib/python3.5/logging/__init__.py", line 336, in getMessage
    msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
  File "/home/anton/miniconda3/envs/shorah/bin/amplian.py", line 429, in <module>
    args.s, args.region, args.diversity)
  File "/home/anton/miniconda3/envs/shorah/bin/amplian.py", line 350, in main
    ret_diri = run_child(diri_exe, diri_args)
  File "/home/anton/miniconda3/envs/shorah/bin/amplian.py", line 63, in run_child
    amplog.error("Child %s terminated by signal" % exe_name, retcode)
Message: 'Child /home/anton/miniconda3/envs/shorah/bin/diri_sampler terminated by signal'
Arguments: (127,)
Traceback (most recent call last):
  File "/home/anton/miniconda3/envs/shorah/bin/amplian.py", line 429, in <module>
    args.s, args.region, args.diversity)
  File "/home/anton/miniconda3/envs/shorah/bin/amplian.py", line 354, in main
    run_diagnostics(win_file, n_reads)
  File "/home/anton/miniconda3/envs/shorah/bin/amplian.py", line 80, in run_diagnostics
    with open(dbg_file) as l:
FileNotFoundError: [Errno 2] No such file or directory: 'w-reference-1-73.dbg'

Savage seems to have incorrect version of `boost`:


savage -s input_fas/singles.fastq -p1 input_fas/paired1.fastq -p2 input_fas/paired2.fastq -m 200 --split 1
/home/anton/miniconda3/envs/savage-bc/opt/savage-0.4.0/bin/ViralQuasispecies: symbol lookup error: /home/anton/miniconda3/envs/savage-bc/opt/savage-0.4.0/bin/ViralQuasispecies: undefined symbol: _ZN5boost15program_options3argE

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nekrut commented 6 years ago

The test data for SHOrah and Savage are contained within their repos. Here are the commands to use for testing.

For shorah:

amplian.py -b  ~/git/shorah/examples/amplicon_test/ampli_sorted.bam -f ~/git/shorah/examples/amplicon_test/reference.fasta -m 0.95

for Savage:

savage -s input_fas/singles.fastq -p1 input_fas/paired1.fastq -p2 input_fas/paired2.fastq -m 200 --split 1

veg / tools-iuc